Re: [gmx-users] how to convert CGenFF into .itp file?

[Peter C. Lai]

It should come with two files. A .prm file, which contains the actual
forcefield parameters that you use the script to convert to bonded and
nonbonded .itp and atomtypes.atp The .rtf file is the charmm equivalent of 
our .rtp file: it contains some premade residue topologies with charge and 
connectivity information. I don't know if there are scripts to convert this or 
not, but it's easy enough to get what you need by hand especially since if 
your ligand isn't in there, you'll have to create the .rtp entry on your own 
or get them from paramchem anyway...

On 2012-12-26 12:29:29PM +0100, Albert wrote:
> On 12/26/2012 12:18 PM, Peter C. Lai wrote:
> > You don't. CGenFF is a forcefield, like CHARMM36. You install it, add rtp
> > entries then use pdb2gmx to generate a ligand's topology .itp file
> 
> THX
> but the problem is how to use this script? I've already download the 
> latest CGenFF file from CHARMM FF websiteIt is a folder.
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Re: [gmx-users] how to convert CGenFF into .itp file?

[Peter C. Lai]

You don't. CGenFF is a forcefield, like CHARMM36. You install it, add rtp
entries then use pdb2gmx to generate a ligand's topology .itp file

On 2012-12-26 11:35:46AM +0100, Albert wrote:
> hello:
> 
> I found the script charmm2gromacs-pvm.py 
>  
> which claimed could convert the output from CGenFF into Gromacs format. 
> However, I tried many times and it always failed even with the advices 
> from previous thread. This script is trying to generate something like 
> what we see in a complete forcefiled folder instead of a single .itp 
> file for ligand.
> 
>I am just wondering, how can we convert the output from CGenFF into a 
> single .itp file which is similar to the one from Swissparam?
> 
> thank you very much
> best
> Albert
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Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

[Peter C. Lai]

You can always see if you have any by looking at cgnr column of the protein
.itp file. If each atom is in its own chargegroup (the cgnr increments by 
atom) then it's fine.

Is this charmm36 (when did you install this from the website?)or 
27 (what gromacs version)? There were two chargegroup problems fixed in two 
successive versions. First, I think 4.5.4 Charmm27 removed all chargegroups
for by default in the .rtp files. Then, the charmm36 upload was fixed to
do that too. However, I am not sure what versions has fixed terminii. 
In gromacs 4.5.3 and the charmm36 from that time period would generate 
capping groups with a single large chargegroup.

Anyway, Grompp will give you an idea if you have a really large chargegroup 
when it gives you the notice about them; if your largest chargegroup is 
comparable to the van der waals diamater of two atoms I don't think there is 
anything to worry about. If you do have a lot of large chargegroups, 
apparently you might run into cutoff artifacts but I'm not sure exactly.


On 2012-12-20 01:37:25PM +0300, James Starlight wrote:
> Peter,
> 
> what errors might occurs if I've missed -nochargegrp option while
> parametrising  my protein by means of pdb2gmx?
> 
> 
> James
> 
> 
> 2012/12/20 Peter C. Lai :
> > (As a side note, Gromacs shouldn't use charge groups when using
> > all-atom charmm forcefields.)
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Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

[Peter C. Lai]

I don't know.

Parachem outputs stuff like this (CHARMM toppar format):

(propionic acid, C3H2O5)

RESI PROA -1.00 
GROUP
ATOM  C2  CG321   -0.28 
ATOM  C1  CG2O30.62 
ATOM  H21 HGA2 0.09 
ATOM  H22 HGA2 0.09   
ATOM  O1  OG2D2   -0.76 
ATOM  O2  OG2D2   -0.76 
GROUP   
ATOM  C3  CG331   -0.27 
ATOM  H31 HGA3 0.09
ATOM  H32 HGA3 0.09
ATOM  H33 HGA3 0.09

BOND C1 C2  C2 C3  C1 O1
BOND C2 H21 C2 H22
BOND C3 H31 C3 H32 C3 H33
DOUBLE  C1 O2
IMPR C1 O2 O1 C2

which you can easily write a script to convert to .rtp (or just convert by
hand) but it'd be more complicated to create an entire .itp from this
format; pdb2gmx will do it if you convert this to .rtp though. I also
frequently encounter ligands that don't have hydrogens too, so that's why
I would write a .hdb entry if necessary.

(As a side note, Gromacs shouldn't use charge groups when using 
all-atom charmm forcefields.)

On 2012-12-20 09:27:12AM +0100, Albert wrote:
> On 12/20/2012 09:13 AM, pcl wrote:
> > Well what works for me is I convert cgenff and merge it with charmm36 (you 
> > only have to do this once per cgenff version), then I have paramchem 
> > generate cgenff charges for the ligand. Then I convert the output of 
> > paramchem (charges) to .rtp format. I also have to create .hdb entries. 
> > Paramchem may also generate additional cgenff atom interactions (dihedrals 
> > or impropers) that may not exist by default, I usually convert and add 
> > those to forcefield's .itp files. Then pdb2gmx will work on the ligand pdb.
> 
> 
> but isn't there is a script to do so in Gromacs webiste, which can 
> convert the output from parachem into Gromacs .itp format? although I 
> didn't try it hard, because I don't find any documentation to use it 
> correctly.
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Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

[Peter C. Lai]

I am not 100% sure how the differences in c36 will affect the parameters you
get from SwissParam.

Personally I prefer to use ParamChem (CHARMM's version of Swissprot) to
give me ligand parameters using CGenFF atomtypes, since I have CGenFF 
merged into my Charmm36 forcefield in gromacs.
 

On 2012-12-19 10:37:40AM +0300, James Starlight wrote:
> Peter, many thanks!
> 
> 
> Could you tell me is there any differences in atom types between
> charmm27 and charmm36 ff? I'd like to simulate receptor-ligand complex
> in that bilayer where ligand molecule would be parametrized by
> Swiss-param ( make topology for the ligands in charmm27 ff). So
> because receptor and bilayer will be parametrized in charmm36 I'm not
> sure about proper working of Swiss's topology with that complex.
> 
> James
> 
> 2012/12/19 Peter C. Lai :
> > http://cesium.hyperfine.info/~peter/gromacs/popc36/
> > has a fully gromacs compatible charmm36 238 POPC bilayer with 21524 waters
> >
> > On 2012-12-18 09:07:22PM -0800, James Starlight wrote:
> >> Justin, thanks again.
> >>
> >> As I understood gromacs already had had parameters for charmm lipid so
> >> the main approach is to do ITP file for 1 lipid by means of pdb2gmx
> >> isnt it?
> >>
> >> By the way is there any way to convert PSF or CRD file to PDB?
> >>
> >> I've found suitable bilayer for my simulation but it lack such coordinates.
> >> POPE Bilayer (310.15K, A=65.2 Â/lipid, 10ns, 340 lipids, noLRCs):
> >> CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
> >>
> >> James
> >>
> >> 2012/12/18, Justin Lemkul :
> >> >
> >> >
> >> > On 12/18/12 2:02 PM, James Starlight wrote:
> >> >> Dear Gromacs Users!
> >> >>
> >> >> I'm looking for 150-200 lipid bilayer ( POPC or POPE) parametrized in
> >> >> charmm27 or charmm36 force field and pre-equilibrated in NPT
> >> >> conditions. I'll bevery thankfull to anybody who provide me with the
> >> >> coordinates as well as itp file for such bilayer.
> >> >>
> >> >
> >> > http://terpconnect.umd.edu/~jbklauda/research/download.html
> >> >
> >> > Google is your friend.  There are plenty more places to look.  A search 
> >> > for
> >> >
> >> > "POPC CHARMM membrane coordinates" (without the quotes) does the trick.
> >> >
> >> > -Justin
> >> >
> >> > --
> >> > 
> >> >
> >> > Justin A. Lemkul, Ph.D.
> >> > Research Scientist
> >> > Department of Biochemistry
> >> > Virginia Tech
> >> > Blacksburg, VA
> >> > jalemkul[at]vt.edu | (540) 231-9080
> >> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >> >
> >> > 
> >> > --
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> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >> >
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Re: [gmx-users] Energy minimization

[Peter C. Lai]

Read through the log file to find out what atoms are causing the system to 
crash. I also prefer running mdrun -v and capturing that too, since it
provides similar log data but does not output the energy tables.

You also did not specify what the final maximum forces were in the system
after the last round of minimization or what atom had the highest force
at the end of the EM.

If you did anything weird with the protein, you may have to go through the 
entire structure sidechain by sidechain to make sure that there are no weird
connectivities (Once I had a peptide bond from a coil going straight through 
the plane of a benzene ring in a far-away residue, and the simulation would 
always crash because the forces of the covalent bonds in the ring would blow
up as it clashed with the forces calculated for the peptide bond and this was 
not noticed during minimization). 

On 2012-12-17 03:04:47AM -0800, Shima Arasteh wrote:
> 
> 
> Dears,
> I changed the coordinates of overlapping atoms and got a normal potential 
> energy. Then when I go to the next step ( NVT equilibrium ), it doesn't run 
> and I just get some pdb files. How is it possible to find the problem?
> 
> It might be clashes in the system but How can I find the overlapping atoms 
> and the reason of clashe among a vast number of atoms?
> 
> 
> Sincerely,
> Shima
> 
> 
> - Original Message -
> From: Peter C. Lai 
> To: Shima Arasteh 
> Cc: Discussion list for GROMACS users 
> Sent: Sunday, December 16, 2012 11:18 AM
> Subject: Re: [gmx-users] Energy minimization
> 
> Probably remove the overlapping lipid then. Once you run MD it will repack.
> 
> On 2012-12-15 09:19:49PM -0800, Shima Arasteh wrote:
> > Thanks for your kind reply.
> > My system is composed of protein packed by lipids. The atoms overlapping, 
> > are protein ( atom 288)  and lipid chain. I think if I move them, I may get 
> > some other clashes, may I not? 
> > Any other suggestion?
> > 
> > Thanks.
> > 
> > 
> >  
> > Sincerely,
> > Shima
> > 
> > 
> > - Original Message -
> > From: Peter C. Lai 
> > To: Shima Arasteh ; Discussion list for 
> > GROMACS users 
> > Cc: 
> > Sent: Sunday, December 16, 2012 8:44 AM
> > Subject: Re: [gmx-users] Energy minimization
> > 
> > It depends on what the atom is overlapping with and some conjecture as to 
> > what might be causing the overlap:
> > 
> > You can always manually move it, either by editing the .gro file directly
> > or using a tool like VMD to move it or the molecule/fragment it's attached 
> > to
> > with the mouse and then display the new coordinates and the update the .gro 
> > file.
> > If it's something like a solvent molecule (water/lipid) and there is 
> > nowhere 
> > to move the molecule, you can try deleting it too (just remmeber to update 
> > .top file).
> > 
> > On 2012-12-15 08:58:59PM -0800, Shima Arasteh wrote:
> > > When I find overlapping atom, what should I have to do? How is it 
> > > possible to get solved?
> > > 
> > > 
> > > Would you please help me? 
> > > 
> > > 
> > > Sincerely,
> > > Shima
> > > 
> > > 
> > > 
> > > From: Justin Lemkul 
> > > To: Shima Arasteh ; Discussion list for 
> > > GROMACS users  
> > > Sent: Saturday, September 29, 2012 3:01 PM
> > > Subject: Re: [gmx-users] Energy minimization
> > > 
> > > 
> > > 
> > > On 9/29/12 3:19 AM, Shima Arasteh wrote:
> > > >
> > > > Dear all,
> > > >
> > > > My system contains lipids, protein and water.
> > > > I want to energy minimize it, so ran grompp:
> > > >
> > > >
> > > > # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
> > > >
> > > > and then:
> > > > # mdrun -v -deffnm em
> > > >
> > > >
> > > > The output is:
> > > > Steepest Descents:
> > > >     Tolerance (Fmax)   =  1.0e+03
> > > >     Number of steps    =        5
> > > > Step=   14, Dmax= 1.2e-06 nm, Epot=  2.30004e+17 Fmax=         inf, 
> > > > atom= 518
> > > > Stepsize too small, or no change in energy.
> > > > Converged to machine precision,
> > > > but not to the requested precision Fmax < 1000
> > > >
> > > > Double precision normally gives you higher accuracy.
> > > > You might need to increase your constraint accurac

Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

[Peter C. Lai]

http://cesium.hyperfine.info/~peter/gromacs/popc36/
has a fully gromacs compatible charmm36 238 POPC bilayer with 21524 waters

On 2012-12-18 09:07:22PM -0800, James Starlight wrote:
> Justin, thanks again.
> 
> As I understood gromacs already had had parameters for charmm lipid so
> the main approach is to do ITP file for 1 lipid by means of pdb2gmx
> isnt it?
> 
> By the way is there any way to convert PSF or CRD file to PDB?
> 
> I've found suitable bilayer for my simulation but it lack such coordinates.
> POPE Bilayer (310.15K, A=65.2 Â/lipid, 10ns, 340 lipids, noLRCs):
> CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD
> 
> James
> 
> 2012/12/18, Justin Lemkul :
> >
> >
> > On 12/18/12 2:02 PM, James Starlight wrote:
> >> Dear Gromacs Users!
> >>
> >> I'm looking for 150-200 lipid bilayer ( POPC or POPE) parametrized in
> >> charmm27 or charmm36 force field and pre-equilibrated in NPT
> >> conditions. I'll bevery thankfull to anybody who provide me with the
> >> coordinates as well as itp file for such bilayer.
> >>
> >
> > http://terpconnect.umd.edu/~jbklauda/research/download.html
> >
> > Google is your friend.  There are plenty more places to look.  A search for
> >
> > "POPC CHARMM membrane coordinates" (without the quotes) does the trick.
> >
> > -Justin
> >
> > --
> > 
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
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> >
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Re: [gmx-users] SDS micelle simulation in TFE solvent

[Peter C. Lai]

On 2012-12-19 10:16:09AM +0530, Archana Sonawani wrote:
> Hi,
> 
>   I want to simulate a peptide using SDS micelle. The peptide is random
> coil,
> but I want it to be helical; therefore, I will use TFE for inducing
> helix.

You use TFE in a wet lab to physically induce helicity in real life. For
a simulation, there is no guarantee that the forcefield you are using will
behave in the same way. Might as well just use distance restraints to force
the helicity. 

> I have never performed simulations using micelle. I have following
> queries:
> 1. *From where would I get coordinates of SDS micelle-water complex? *(
> I
> have .itp file for SDS)

the g_membed introduciton page has an example of embedding in a POPE micelle.
http://wwwuser.gwdg.de/~ggroenh/membed.html

You can probably conduct a literature search and find a paper that provides
a pdb for an SDS micelle.


> 2. Do I require lipid.itp for this simulation?

you say you already have a .itp for SDS that works your chosen forcefield?

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Re: [gmx-users] Energy minimization

[Peter C. Lai]

Probably remove the overlapping lipid then. Once you run MD it will repack.

On 2012-12-15 09:19:49PM -0800, Shima Arasteh wrote:
> Thanks for your kind reply.
> My system is composed of protein packed by lipids. The atoms overlapping, are 
> protein ( atom 288)  and lipid chain. I think if I move them, I may get some 
> other clashes, may I not? 
> Any other suggestion?
> 
> Thanks.
> 
> 
>  
> Sincerely,
> Shima
> 
> 
> ----- Original Message -
> From: Peter C. Lai 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Cc: 
> Sent: Sunday, December 16, 2012 8:44 AM
> Subject: Re: [gmx-users] Energy minimization
> 
> It depends on what the atom is overlapping with and some conjecture as to 
> what might be causing the overlap:
> 
> You can always manually move it, either by editing the .gro file directly
> or using a tool like VMD to move it or the molecule/fragment it's attached to
> with the mouse and then display the new coordinates and the update the .gro 
> file.
> If it's something like a solvent molecule (water/lipid) and there is nowhere 
> to move the molecule, you can try deleting it too (just remmeber to update 
> .top file).
> 
> On 2012-12-15 08:58:59PM -0800, Shima Arasteh wrote:
> > When I find overlapping atom, what should I have to do? How is it possible 
> > to get solved?
> > 
> > 
> > Would you please help me? 
> > 
> > 
> > Sincerely,
> > Shima
> > 
> > 
> > 
> > From: Justin Lemkul 
> > To: Shima Arasteh ; Discussion list for 
> > GROMACS users  
> > Sent: Saturday, September 29, 2012 3:01 PM
> > Subject: Re: [gmx-users] Energy minimization
> > 
> > 
> > 
> > On 9/29/12 3:19 AM, Shima Arasteh wrote:
> > >
> > > Dear all,
> > >
> > > My system contains lipids, protein and water.
> > > I want to energy minimize it, so ran grompp:
> > >
> > >
> > > # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
> > >
> > > and then:
> > > # mdrun -v -deffnm em
> > >
> > >
> > > The output is:
> > > Steepest Descents:
> > >     Tolerance (Fmax)   =  1.0e+03
> > >     Number of steps    =        5
> > > Step=   14, Dmax= 1.2e-06 nm, Epot=  2.30004e+17 Fmax=         inf, atom= 
> > > 518
> > > Stepsize too small, or no change in energy.
> > > Converged to machine precision,
> > > but not to the requested precision Fmax < 1000
> > >
> > > Double precision normally gives you higher accuracy.
> > > You might need to increase your constraint accuracy, or turn
> > > off constraints alltogether (set constraints = none in mdp file)
> > >
> > > writing lowest energy coordinates.
> > >
> > > Back Off! I just backed up em.gro to ./#em.gro.3#
> > >
> > > Steepest Descents converged to machine precision in 15 steps,
> > > but did not reach the requested Fmax < 1000.
> > > Potential Energy  =  2.3000388e+17
> > > Maximum force     =            inf on atom 518
> > > Norm of force     =            inf
> > >
> > > It seems that atome 518 has an infinite energy. So I tried to apply the 
> > > suggestion of turning off the constraints in em.mdp. To do so, I added 
> > > "constraints=none" to mdp file, But it doesn't make different.
> > >
> > > Any suggestion please? I don't know how to solve this problem. Please 
> > > help me.
> > >
> > 
> > Atom 518 is overlapping with something nearby.  You will have to visualize 
> > the 
> > system to identify the source of the problem.
> > 
> > -Justin
> > 
> > -- 
> > 
> > 
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > 
> >  
> > -- 
> > gmx-users mailing list    gmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at 
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
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Re: [gmx-users] Energy minimization

[Peter C. Lai]

It depends on what the atom is overlapping with and some conjecture as to 
what might be causing the overlap:

You can always manually move it, either by editing the .gro file directly
or using a tool like VMD to move it or the molecule/fragment it's attached to
with the mouse and then display the new coordinates and the update the .gro 
file.
If it's something like a solvent molecule (water/lipid) and there is nowhere 
to move the molecule, you can try deleting it too (just remmeber to update 
.top file).

On 2012-12-15 08:58:59PM -0800, Shima Arasteh wrote:
> When I find overlapping atom, what should I have to do? How is it possible to 
> get solved?
> 
> 
> Would you please help me? 
> 
> 
> Sincerely,
> Shima
> 
> 
> 
> From: Justin Lemkul 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users  
> Sent: Saturday, September 29, 2012 3:01 PM
> Subject: Re: [gmx-users] Energy minimization
> 
> 
> 
> On 9/29/12 3:19 AM, Shima Arasteh wrote:
> >
> > Dear all,
> >
> > My system contains lipids, protein and water.
> > I want to energy minimize it, so ran grompp:
> >
> >
> > # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
> >
> > and then:
> > # mdrun -v -deffnm em
> >
> >
> > The output is:
> > Steepest Descents:
> >     Tolerance (Fmax)   =  1.0e+03
> >     Number of steps    =        5
> > Step=   14, Dmax= 1.2e-06 nm, Epot=  2.30004e+17 Fmax=         inf, atom= 
> > 518
> > Stepsize too small, or no change in energy.
> > Converged to machine precision,
> > but not to the requested precision Fmax < 1000
> >
> > Double precision normally gives you higher accuracy.
> > You might need to increase your constraint accuracy, or turn
> > off constraints alltogether (set constraints = none in mdp file)
> >
> > writing lowest energy coordinates.
> >
> > Back Off! I just backed up em.gro to ./#em.gro.3#
> >
> > Steepest Descents converged to machine precision in 15 steps,
> > but did not reach the requested Fmax < 1000.
> > Potential Energy  =  2.3000388e+17
> > Maximum force     =            inf on atom 518
> > Norm of force     =            inf
> >
> > It seems that atome 518 has an infinite energy. So I tried to apply the 
> > suggestion of turning off the constraints in em.mdp. To do so, I added 
> > "constraints=none" to mdp file, But it doesn't make different.
> >
> > Any suggestion please? I don't know how to solve this problem. Please help 
> > me.
> >
> 
> Atom 518 is overlapping with something nearby.  You will have to visualize 
> the 
> system to identify the source of the problem.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>  
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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Re: [gmx-users] gold-S simulation

[Peter C. Lai]

Where is the .itp file for the system?

On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote:
> hi 
> 
> 
> I'm simulating gold atom interaction with  aminoacidcys. I have made 
> gold-cys.pdb by hyperchem software:
> 
> HETATM    1  N   CYS 1   0.000   1.335   0.000
> HETATM    2  CA  CYS 1  -0.683   1.818  -1.183
> HETATM    3  C   CYS 1  -0.705   3.339  -1.221
> HETATM    4  O   CYS 1  -0.184   3.993  -0.319
> HETATM    5  CB  CYS 1  -2.127   1.330  -1.221
> HETATM    6  SG  CYS 1  -3.106   1.859  -2.649
> HETATM    8 AU   AU  8  -2.833   0.428  -1.793
> HETATM    9 AU   AU  9  -2.647   0.381  -2.869
> HETATM   10 AU   AU 10  -1.691   1.360  -3.093
> HETATM   11 AU   AU 11  -0.647   2.706  -2.135
> HETATM   12 AU   AU 12  -2.742   0.834  -0.456
> HETATM   13 AU   AU 13  -1.691   2.061  -0.043
> HETATM   14 AU   AU 14  -0.783   3.136   0.376
> HETATM   15 AU   AU 15   0.095   3.750  -1.068
> HETATM   16 AU   AU 16  -2.929   2.480  -2.204
> HETATM   17 AU   AU 17  -3.285   1.594  -3.328
> HETATM   18 AU   AU 18  -2.544   2.593  -3.763
> HETATM   19 AU   AU 19  -1.951   1.260  -2.303
> CONECT    1    2
> CONECT    0    1
> CONECT    2    1    3    5
> CONECT    0    2
> CONECT    3    2    4
> CONECT    4    3
> CONECT    5    2    6
> CONECT    0    5
> CONECT    0    5
> CONECT    6    5
> CONECT    0    6
> CONECT    0    6
> CONECT    0    6
> END
> 
>  
> 
> I started simulation by this pdb file. I'm using OPLSAA force field and also 
> I added gold parameter in ffnonbonded.itp  :
> .
> .
> .
> ; Added by DvdS 05/2005 copied from GROMACS force field.   
>  SI SI 14    28.08000 0.000    A    3.38550e-01  
> 2.44704e+00
>  AU AU 79   196.9700 0.000   A    0.29510e+00  22.1120e+00
> 
> [ nonbond_params ]
> AU  AU   1    0.0e+00  0.0e+00
> 
> 
> ; SC 08/2007: Special Au-N vdw to simulate chemical bond between 
> gold-imidazole
>  AU opls_511 1    3.07000e-01  3.96000e+00
>  
> ; SC 05/2008: special Au-C and Au-H to simulate pi-systems alkenes+benzene 
> (and PHE)
>  AU opls_142 1    3.21000e-1   2.65400e+00
>  AU opls_143 1    3.21000e-1   2.65400e+00
>  AU opls_144 1    2.67000e-1   1.66500e+00
>  AU opls_145 1    3.2e-1   2.54600e+00
>  AU opls_146 1    2.67000e-1   1.66500e+00
>  AU opls_150 1    3.21000e-1   2.65400e+00
>  
> ; +imidazole and His
>  AU opls_506 1    3.21000e-1   2.54000e+00
>  AU opls_507 1    3.21000e-1   2.54000e+00
>  AU opls_508 1    3.21000e-1   2.54000e+00
> 
> ; +HisH
>  AU opls_509 1    3.21000e-1   2.54000e+00
>  AU opls_510 1    3.21000e-1   2.54000e+00
> ; +TYR
>  AU opls_166 1    3.21000e-1   2.54000e+00
> ; +TRP
>  AU opls_500 1    3.21000e-1   2.54000e+00
>  AU opls_514 1    3.21000e-1   2.54000e+00
>  AU opls_501 1    3.21000e-1   2.54000e+00
>  AU opls_502 1    3.55000e-1   3.55000e+00
> 
> and I concidered AU-S as bonding connection and I added its parameter (bond 
> stretch, dihedral and angle ) in ffbonded.itp file: 
> [ bondtypes ]
> ; i    j  func   b0  kb
> .
> .
> .
> AU    SH  1    0.24000   165528.0   ;
> AU    S   1    0.24000   165528.0   ;
> AU    SG  1    0.24000   165528.0   ;
> .
> .
> .
> [ angletypes ]
> ;  i    j    k  func   th0   cth
> .
> .
> .
>   AU SG CB  1   109.00 46.34
>   AU SH CB  1   109.00 46.34
>   AU S  CB  1   109.00 46.34
> .
> .
> .
> [ dihedraltypes ]
> .
> .
> .
> #define improper_AU_S_CB_CA    -180.0  1.2958 2 
> 
> #define improper_AU_SH_CB_CA   -180.0  1.2958 2
> 
> #define improper_AU_SG_CB_CA    -180   1.2958 2
> 
> #define improper_AU_S_C_C 19   0.9196 2
> 
> #define improper_AU_SH_C_C    19   0.9196 2
> 
> #define improper_AU_SG_C_C    19   0.9196 2
> .
> .
> .
> 
> when I run my simulation I dont see any interaction or affinity between gold 
> atom and S atom of cystein, while it is clear that gold shoud has interaction 
> with sulfur. what is its reason? I'm completely confused. I tried anythings 
> that I can but my system doesn't work.
> 
> please help me
>  
> 
> Fatemeh Ramezani
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

[Peter C. Lai]

On 2012-12-08 03:20:54AM -0800, James Starlight wrote:
> 1- on what assumptions that blocks were generated ?

This appears to be a swissparm-specific question. I don't know what
algorithms it uses to match what are essentially pharmacophores in the new
molecule with the common individual blocks it finds.

> 2- Why charge in [ atomtypes ]  (zero) differes from  the charges in

Because gromacs ignores charges in [atomtypes], so the easiest thing is to
just assign all zeros to that column.

> the topology of the same groups? how I can check correctness of charge
> distribution in such itp files ?

Compare to analogous molecules and see if there are published charges. 
You can also use the building blocks and manually assign charges and see what 
you end up with as well. To be totally rigorous, parameterize the structure 
using a quantum chemistry package and compare the ab initio charge 
distributions to the ones assigned by SwissParm (or by hand).

> 3- What is sigma andepsilon in the [ atomtypes ] ? :)

LJ interactions in sigma-epsilon form. See gromacs manual section 4.1.1

> 4- Have anybody else used Swiss param for modeling protein-ligands
> systems? Might it be used with the charmm36 set ?
> 

CHARMM has its own generalized forcefield (CGenFF) for ligands and other 
molecules, although charmm36 may have cAMP in their nucleotides section...
You can try to also build it using adenine, ribose, and add phosphate.

CGenFF and C36 are interoperable for intermolecular interactions, so if
using CGenFF to paramterize cAMP you would use ParamChem to assign charges 
and then convert and add the CGenFF forcefield parameters (from the gromacs
contributions website) to C36. There are mailing list archives that show
you the script to use to do the CGenFF conversion.



> James
> 
> 2012/12/7, Justin Lemkul :
> >
> >
> > On 12/7/12 2:21 PM, James Starlight wrote:
> >> Justin,
> >>
> >> with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2
> >> rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp
> >>
> >> NOTE 1 [file ./mdps/em.mdp]:
> >>For energy conservation with switch/shift potentials, rlist should be
> >> 0.1
> >>to 0.3 nm larger than rvdw.
> >>
> >> NOTE 2 [file ./mdps/em.mdp]:
> >>The sum of the two largest charge group radii (0.078024) is larger
> >> than
> >>rlist (1.20) - rvdw (1.20)
> >>
> >
> > As I recall, there is a small bug where grompp ignores rlistlong when
> > printing
> > this message.  The simulation will be fine.
> >
> > -Justin
> >
> >>
> >> Should I increase Rlist to the 1.4 ( as well as rcoulomb to the same
> >> value because of PME) ?
> >>
> >> 2012/12/7, Justin Lemkul :
> >>>
> >>>
> >>> On 12/7/12 1:19 PM, James Starlight wrote:
>  Justin,
> 
>  following to your advise I've tried to use charmm 27 ff for simulation
>  of my protein-cGMP complex ( ligand was parametrized by Swiss Param
>  server).
> 
>  Could you provide me with the cut-offs for vdw as well as
>  electrostatics suitable for simulation in charmm27 and 36 force
>  fields?
> 
> >>>
> >>> http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html
> >>>
>  Does anybody know another servers for parametrization of the ligands
>  for charmm simulation in gromacs?
> 
> >>>
> >>> If Google can't find it, it probably doesn't exist.
> >>>
> >>> -Justin
> >>>
>  2012/12/7, Justin Lemkul :
> >
> >
> > On 12/7/12 11:42 AM, James Starlight wrote:
> >> Justin,
> >>
> >> ligand-only simulation in vacuum have been finished with the same
> >> errors
> >> :)
> >>
> >> Step 19200, time 38.4 (ps)  LINCS WARNING
> >> relative constraint deviation after LINCS:
> >> rms 0.025443, max 0.140660 (between atoms 1 and 3)
> >> bonds that rotated more than 30 degrees:
> >> atom 1 atom 2  angle  previous, current, constraint length
> >>  1  2   52.20.1033   0.0985  0.1000
> >>  1  3   90.10.1168   0.1141  0.1000
> >>
> >> Step 19200, time 38.4 (ps)  LINCS WARNING
> >> relative constraint deviation after LINCS:
> >> rms 0.025376, max 0.140474 (between atoms 1 and 3)
> >> bonds that rotated more than 30 degrees:
> >> atom 1 atom 2  angle  previous, current, constraint length
> >>  1  2   52.00.1033   0.0988  0.1000
> >>  1  3   90.00.1168   0.1140  0.1000
> >> step 19200, will finish Sat Dec  8 04:10:49 2012
> >> Step 19201, time 38.402 (ps)  LINCS WARNING
> >> relative constraint deviation after LINCS:
> >> rms 0.052715, max 0.293316 (between atoms 1 and 3)
> >> bonds that rotated more than 30 degrees:
> >> atom 1 atom 2  angle  previous, current, constraint length
> >>  1  2   49.30.0988   0.0993  0.1000
> >>  1  3   90.00.1140   0.1293  0.1000
> >>
> >> Ste

Re: [gmx-users] area per lipid

[Peter C. Lai]

Not if you aren't going to run those. I assume nvt.mdp and npt.mdp are 
restrained runs to remove/dampen clashes and prevent crashes but if you are
already running a full md simulation then you don't need to redo those steps.

Also, I don't use DispCorr for C36 lipids (some debates about that can be
found on the gromacs mailing list in the past). Setting the constraints to
hbonds and using a TIPS3P water model can also help get POPC APL closer
to experiment, especially if the starting configuration was highly ordered.

On 2012-12-07 10:56:33PM -0800, Shima Arasteh wrote:
> Hi again,
> 
> I edited my md.mdp files. I'm wondering if my nvt.mdp and npt.mdp in charmm36 
> ff also need such a edition? 
> Also I'd like to know if these mdp file are applicable in any simulation done 
> with charmm36?
> 
> 
> 
> Sincerely,
> Shima
> 
> 
> From: Justin Lemkul 
> To: Shima Arasteh  
> Sent: Friday, November 9, 2012 3:49 PM
> Subject: Re: [gmx-users] area per lipid
> 
> 
> 
> On 11/9/12 1:46 AM, Shima Arasteh wrote:
> >
> >
> > I pick the snapshots every 10ns, because I don't know how much time this 
> > system needs to be simulated to reach to the proper APL.
> >
> 
> What I'm saying is there are far better ways to assess any trends in your 
> data 
> rather than taking 4 snapshots along a much larger trajectory.  You can 
> gather a 
> lot more detail, and very easily.  You're saving snapshots every 2 ps, which 
> means you will have 2 data points that can be analyzed, rather than just 
> 4.
> 
> > The md.mdp dile I used here is:
> >
> > title        = Production run for Water-POPC system
> >
> > ; Parameters describing the details of the NVT simulation protocol
> > integrator    = md
> > dt        = 0.002
> > nsteps        = 500
> >
> > ; Parameters controlling output writing
> > nstxout        = 1000
> > nstvout        = 1000
> > nstenergy    = 1000
> > nstlog        = 1000
> >
> > ; Parameters describing neighbors searching and details about interaction 
> > calculations
> > ns_type        = grid
> > nstlist        = 5
> > rlist        = 1.2
> > rcoulomb    = 1.2
> > rvdw        = 1.2
> > pbc        = xyz
> >
> 
> You're using a plain cutoff for the van der Waals interactions, which is 
> incorrect for the CHARMM force fields.  You need the following:
> 
> vdwtype = switch
> rvdw_switch = 0.8
> rvdw = 1.2
> rlistlong = 1.4
> 
> The other settings are fine.
> 
> -Justin
> 
> > ; Parameters for treating bonded interactions
> > continuation    = yes
> > constraint_algorithm = LINCS
> > constraints    = all-bonds
> > lincs_iter    = 1
> > lincs_order    = 4
> >
> > ; Parameters for treating electrostatic interactions
> > coulombtype    = PME
> > pme_order    = 4
> > fourierspacing    = 0.16
> >
> > ; Temperature coupling parameters
> > tcoupl        = Nose-Hoover
> > tc-grps        = POPC SOL
> > tau_t        = 0.5    0.5
> > ref_t        = 300     300
> >
> > ; Pressure coupling parameters
> > pcoupl        = Parrinello-Rahman
> > pcoupltype    = semiisotropic
> > tau_p        = 2.0
> > ref_p        = 1.0    1.0
> > compressibility = 4.5e-5    4.5e-5
> >
> >
> > DispCorr    = EnerPres
> > gen_vel        = no
> > nstcomm        = 1
> > comm_mode    = Linear
> > comm_grps    =POPC SOL
> >
> >
> >
> > Sincerely,
> > Shima
> >
> >
> > 
> > From: Justin Lemkul 
> > To: Shima Arasteh ; Discussion list for 
> > GROMACS users 
> > Sent: Friday, November 9, 2012 12:20 AM
> > Subject: Re: [gmx-users] area per lipid
> >
> >
> >
> > On 11/8/12 4:39 AM, Shima Arasteh wrote:
> >> Hi,
> >>
> >> I am trying to simulate POPC in water in 300 K, using charmm36 FF. In 
> >> order to reach appropriate area per lipid ( 63-65 Angestroms per headgroup 
> >> as mentioned in articles ), I let the system to be simulated for 40 
> >> seconds. To do so, I checked the area  per lipid every 10 ns. The results 
> >> of area per lipid in each step are as below:
> >>
> >> 1.
> >> Top leaflet: 60.44
> >>
> >> Bottom leaflet: 59.43
> >>
> >>
> >> 2.
> >> Top leaflet: 61.135
> >> Bottom leaflet: 60.11
> >>
> >> 3.
> >> Top leaflet: 61.40
> >>
> >> Bottom leaflet: 60.38
> >>
> >> 4.
> >> Top leaflet: 60.27
> >>
> >> Bottom leaflet: 59.27
> >>
> >> I expected it to approaches the expected amount steadily, but why did I 
> >> get such a result? How can I get to the appropriate area  per lipid?
> >>
> >> Would you please give me suggestions? Any suggestions would be appreciated.
> >>
> >
> > Without seeing a complete .mdp file, it's hard to say.  Why are you picking
> > snapshots every 10 ns?  You can easily plot APL over time for the entire
> > trajectory using the box vectors stored in the .edr file from (Box-X *
> > Box-Y)/(number of lipids).  You would have to write your own script to do 
> > the
> > calculation, but it's quite straightforward.
> >
> > -Justin
> >
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of B

Re: [gmx-users] barium ion simulation

[Peter C. Lai]

You should ask the CHARMM forum to see if anyone there has derived Ba2+
parameters that can then be converted to gromacs.

On 2012-12-02 02:31:27PM -0600, ram bio wrote:
> Dear Gromacs Users,
> 
> I am trying to simulate a protein in lipid bilayer with a barium ion
> binding pocket in it, with Charmm27 FF in gromacs 4.5.4. I found that
> barium ion is not included under charmm27 ff ions.itp. I was wondering
> if there is any way to simulate protein with barium bound using
> gromacs and charmm27 ff?
> 
> Thanks
> Pramod
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] How to avoid adding ions close to ligand

[Peter C. Lai]

There is nothing stopping you from replacing the ion in your binding
pocket with the original water and then replacing another water elsewhere
with the ion at the oxygen's coordintes, then running genconf to renumber
the gro file.

On 2012-11-26 06:25:47PM -0800, Yun Shi wrote:
> I did hope the ions will move out eventually.
> 
> But after my ~70ns of conventional MD (with duplicate MD runs and the
> protein as a dimer with identical sequence), they were still there in
> the binding site.
> 
> So I assume it would be much better to start without any salt ions
> beside my ligand.
> 
> Could anyone suggest a way around this?
> 
> Thanks,
> Yun
> 
> On Mon, Nov 26, 2012 at 12:39 PM, David van der Spoel
>  wrote:
> > On 2012-11-26 21:28, Yun Shi wrote:
> >>
> >> Hi everyone,
> >>
> >> I am doing conventional MD of a protein-ligand system with a mobile
> >> loop as part of the binding site.
> >>
> >> Presumably, the positive Arg side chain on the mobile loop will
> >> eventually move towards the negative carboxylic group on my ligand.
> >> But I found the addition of NaCl (0.15 M conc.) had some effect on
> >> this movement, since the random addition could put Na+ or Cl- ions
> >> between the mobile loop and my ligand.
> >>
> >> I tried generating a index containing only SOL far not close to my
> >> ligand, but apparently genion requires a continuous solvent group. So
> >> is there any other way to achieve this? Trying different numbers for
> >> -seed option seems inefficient and is dependent on luck.
> >>
> >> Thanks,
> >> Yun
> >>
> > Maybe your assumption is wrong?
> >
> > Run a long MD simulation and you will find out.
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> > --
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Re: [gmx-users] a question on trajcat settime

[Peter C. Lai]

There is no need to use -settime. trjcat automagically takes the time of the 
last frame from the previous file and starts the next segment of the output 
file with it.


On 2012-11-04 08:46:29PM -0800, Acoot Brett wrote:
> Dear All
> 
> First I ran a 5 ns MD (md-0ns-5ns), I get md-0ns-5ns.tpr and 
> md-0ns-5ns.cpt,then I extend it for 1 ns by
> 
> tpbconv -s tpbconv -s md-0ns-5ns.tpr -extend 1000 -o md-5ns-to-6ns.tpr
> 
> mdrun -deffnm md-5ns-to-6ns -cpi md-0ns-5n.cpt 
> 
> Then I further extend it for 2 ns by 
> 
> tpbconv -s md-5ns-to-6ns.tpr -extend 2000 -o md-6ns-to-8ns.tpr
> 
> mdrun -deffnm md-6ns-to-8ns -cpi md-5ns-to-6ns.cpt 
> 
> Then I connect the md-0ns-5ns.trr, md-5ns-to-6ns.trr, md-6ns-to-8ns.trr by 
> "trajcat -f md-0ns-5ns.trr, md-5ns-to-6ns.trr, md-6ns-to-8ns.trr -o 
> md-0ns-8ns.trr -settime".
> 
> Will you please explain to me on hoe to use "-settime"? Should I input 
> "0,5000,6000"? or something else in order to connect the 3 trr files in time 
> sequence from 0 ns to 8 ns?
> 
> I am looking forward to getting your reply.
> 
> Cheers,
> 
> Acoot
> 
> 
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Re: [gmx-users] Re: are wall atoms virtual ?

[Peter C. Lai]

Wall atoms are virtual in the sense that they are just special Z-axis 
boundary conditions based on the integration of the LJ potential parameterized 
by the atom type, integraton model, and specified density of the "wall". The
particles don't physically exist so you will not see them in VMD (because 
they are just a modification to the simulation box itself and don't show 
up in the coordinate file). I never got around to scripting pbctools to 
dynamically update the box outlines frame by frame either, but there is
probably a way to do that. Theoretically, your walls would be seen where the
lines are showing the top and bottom of the box :)


On 2012-11-01 10:37:43AM -0700, harshaljain950 wrote:
> I have defined the wall by adding nwall option in my mdp file, I didn't
> name it as 'carbon wall'. I just use this name to refer to this wall in
> discussions
> 
> Do you have any documentation or tutorial regarding implementation of
> walls, I am in a great need of one as i am new to gromacs
> 
> Thank you for replying
> 
> 
> 
> 
> --
> View this message in context: 
> http://gromacs.5086.n6.nabble.com/are-wall-atoms-virtual-tp5002549p5002561.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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[gmx-users] g_rms/rmsf: fit vs. nofit

[Peter C. Lai]

Hi

I have sort of a noob question about when to fit and when not to fit when 
computing rmsd and rmsf.

My use-case is to look at the motion of different domains of a protein
where there are atoms near the COM of the starting structure that remain 
relatively stable throughout the simulation according to g_traj. 

Right now, I have been using trjconv -center the trajectory on this core alpha
carbon then using trjconv -dump and grompp to generate a recentered starting
structure .tpr. Then I am running g_rms or g_rmsf -nofit against the recentered
.tpr as the reference.

Is this wildly inappropriate? Should I be fitting against an index group
consisting of that atom instead? Because the backbone is supposed to be 
shifting I want to minimize any artifacts that would potentially dampen an 
observable residue motion just because the rmsd was computed after a fit,
and centering the trajectory on an atom near the starting COM would minimize
distances traveled due to COM diffusion through the solvent.

-- 
==
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Programmer/Analyst  | KAUL 752A
Genetics Div. of Research   | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Type 9 dihedral in Gromacs topology

[Peter C. Lai]

On 2012-10-27 01:20:15PM -0400, Andrew DeYoung wrote:
> (1) What is a type 9 dihedral?  On page 74 of Section 4.2.12 of the manual,
> it says, "For certain force fields, type 9 is useful.  Type 9 allows
> multiple potential functions to be applied automatically to a single
> dihedral in the [ dihedral ] section when multiple parameters are defined
> for the same atomtypes in the [ dihedraltypes ] section."  What does this
> mean?  What does it mean to apply multiple potential functions to a single
> dihedral?  Is this a fundamentally different way of specifying a dihedral?
> 

It means what it says. Look at the charmm's ffbonded.itp file closely again,
in the dihedral section. You will see that for each combination of dihedral
angles, you can have multiple potentials defined with different 
multiplicities. In a non-type 9 dihedral potential gromacs would complain 
about a second dihedral definition for the same dihedral and override the 
first. Example:

CE2 CE1 CT2 CT3 9   180.00  2.092   1
CE2 CE1 CT2 CT3 9   180.00  5.4392  3

> (2) In that above example from the CHARMM ffbonded.itp, what is the "cp"
> column?  Table 5.5 of on page 125 of Section 5.7 of the manual seems to say
> that in type 9, phi_s, k_phi, and the multiplicity are specified.  Does this
> mean that "cp" corresponds to the force constant k_phi?

Yes, although the CHARMM people call it KChi.


-- 
==========
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
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Re: [gmx-users] Box size/type confusion for bilayer system

[Peter C. Lai]

On 2012-10-18 03:58:22PM -0400, Justin Lemkul wrote:
> 
> 
> On 10/18/12 3:55 PM, Peter C. Lai wrote:
> > On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote:
> >>
> >>
> >> On 10/18/12 2:43 PM, klexa wrote:
> >>> Hi Gromacs users,
> >>>
> >>> I think I am a bit confused about the proper way to handle boxes that are 
> >>> not
> >>> standard cubes. I'm trying to run a membrane simulation where a cyclic
> >>> undecapeptide is inserted into the membrane and I want the water layer to 
> >>> be
> >>> sufficiently thick that if it were pulled, the peptide could be fully 
> >>> solvated
> >>> by the water. To avoid having an enormous box of membrane and water, I 
> >>> have an
> >>> orthorhombic box containing my peptide and bilayer. It minimizes alright 
> >>> with
> >>> Gromacs, but when I go to equilibrate it it fails because it's too skewed 
> >>> to be
> >>> a triclinic box. I've tried modifying the box with editconf and 
> >>> converting it to
> >>> a rhombic dodecahedron, sort of like the manual suggests for a membrane 
> >>> system.
> >>> I'm not sure that even that is sensible since it seems like I would be 
> >>> losing
> >>> content that way, yet nothing is clipped, and I did this after using 
> >>> trjconv to
> >>> remove any periodicity from my prior simulation of this system (in 
> >>> Desmond) but
> >>> doing so gives me a starting potential energy of NaN for the new system 
> >>> that I
> >>> obviously cannot work around. Is what I am trying to do even possible? If 
> >>> it is,
> >>> it seems like there is probably a better way than the way I chose, so if 
> >>> you
> >>> have any suggestions, I would be greatly appreciative.
> >>>
> >>
> >> I have never produced a membrane system with a hexagonal cross-section 
> >> like the
> >> manual describes.  The most straightforward approach in my mind is simply a
> >> rectangular box.  It will save you a ton of headaches.
> >>
> >>> I'm trying to run this simulation with AMBER FF99SB parameters for the 
> >>> peptide,
> >>> Tieleman's lipid parameters for POPC, and SPCE waters, so just as a sanity
> >>> check, is it reasonable to consider a system like that?
> >>>
> >>
> >> I don't know how this would even run.  The AMBER protein force field and 
> >> Berger
> >> lipid paramters use different combination rules, and I have never seen a
> >> demonstration that one can use them together.  It is most straightforward 
> >> to use
> >> a Gromos force field or OPLS-AA with modifications to account for the 
> >> changes in
> >> combination rules.
> >
> > Or just use a self-consistent FF and setup already published/validated for
> > such a system, like AMBER+GAFF or CHARMM+CGENFF. The choice of forcefield
> > combinations for a peptide-membrane system doesn't require completely
> > reinventing the wheel these days.
> >
> 
> One doesn't even need CGENFF for this; there are very good lipid parameters 
> within the latest editions of the CHARMM force fields.  My suggestion was 
> motivated by the mention of the Berger lipids that the OP was already trying 
> to 
> use.  Has anyone produced good lipid parameters using GAFF?  I recall seeing 
> one 
> or two papers a few years ago, but I think there was considerable refinement 
> after the initial parameterization.

I was thinking along the lines of CHARMM for the bilayer and CGENFF for his
molecule (although rereading it sounds like he's just using standard
polypeptides, so yeah C36 for everything is probalby the way to go).

For Amber systems I thought people used a recent GAFF for the bilayer and 
Amber for the peptide. There was a 2010 or 2011 Plos paper on Beta2 
Adrenergic receptor that used a GAFF POPC bilayer and was run for 700ns.

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Re: [gmx-users] Box size/type confusion for bilayer system

[Peter C. Lai]

On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote:
> 
> 
> On 10/18/12 2:43 PM, klexa wrote:
> > Hi Gromacs users,
> >
> > I think I am a bit confused about the proper way to handle boxes that are 
> > not
> > standard cubes. I'm trying to run a membrane simulation where a cyclic
> > undecapeptide is inserted into the membrane and I want the water layer to be
> > sufficiently thick that if it were pulled, the peptide could be fully 
> > solvated
> > by the water. To avoid having an enormous box of membrane and water, I have 
> > an
> > orthorhombic box containing my peptide and bilayer. It minimizes alright 
> > with
> > Gromacs, but when I go to equilibrate it it fails because it's too skewed 
> > to be
> > a triclinic box. I've tried modifying the box with editconf and converting 
> > it to
> > a rhombic dodecahedron, sort of like the manual suggests for a membrane 
> > system.
> > I'm not sure that even that is sensible since it seems like I would be 
> > losing
> > content that way, yet nothing is clipped, and I did this after using 
> > trjconv to
> > remove any periodicity from my prior simulation of this system (in Desmond) 
> > but
> > doing so gives me a starting potential energy of NaN for the new system 
> > that I
> > obviously cannot work around. Is what I am trying to do even possible? If 
> > it is,
> > it seems like there is probably a better way than the way I chose, so if you
> > have any suggestions, I would be greatly appreciative.
> >
> 
> I have never produced a membrane system with a hexagonal cross-section like 
> the 
> manual describes.  The most straightforward approach in my mind is simply a 
> rectangular box.  It will save you a ton of headaches.
> 
> > I'm trying to run this simulation with AMBER FF99SB parameters for the 
> > peptide,
> > Tieleman's lipid parameters for POPC, and SPCE waters, so just as a sanity
> > check, is it reasonable to consider a system like that?
> >
> 
> I don't know how this would even run.  The AMBER protein force field and 
> Berger 
> lipid paramters use different combination rules, and I have never seen a 
> demonstration that one can use them together.  It is most straightforward to 
> use 
> a Gromos force field or OPLS-AA with modifications to account for the changes 
> in 
> combination rules.

Or just use a self-consistent FF and setup already published/validated for 
such a system, like AMBER+GAFF or CHARMM+CGENFF. The choice of forcefield 
combinations for a peptide-membrane system doesn't require completely 
reinventing the wheel these days.

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Re: [gmx-users] Re: The problem of converting CGenff parameters to those of Gromacs

[Peter C. Lai]

Just to let you know, charge information in ffnonbonded.itp is ignored. 
pdb2gmx reads charges from the corresponding .rtp file when writing the .gro
file.

On 2012-10-16 06:47:57AM -0700, spin wrote:
> Hi, Peter and David,
> 
> Thank you for your help! I have solve it by David's script.
> 
> Qing Liu
> 
> 
> 
> --
> View this message in context: 
> http://gromacs.5086.n6.nabble.com/The-problem-of-converting-CGenff-parameters-to-those-of-Gromacs-tp5002042p5002079.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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======
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] The problem of converting CGenff parameters to those of Gromacs

[Peter C. Lai]

Isn't Mark's script outdated for this purpose?

charmm forcefields specify epsilon and sigmas so you only need to convert 
them:

gromacs(sigma) = (charmm(Rmin/2)/10) * (2/(2^(1/6)))
gromacs(epsilon) = charmm(eps) * 4.184

For 1-4 pair interactions,
gromacs(sigma1,4 i,j) = (charmm(Rmin/2_1,4_i) + charmm(Rmin/2_1,4_j))/(2^1/6)

gromacs(eps1,4 i,j) = sqrt(charmm(eps_1,4_i) * charmm(eps_1,4_j)) * 4.184

On 2012-10-15 07:27:51AM -0700, spin wrote:
> Hello, everyone.
> 
> I used the Mark's script's to convert the CGenff (version 2b7 ) parameter
> file to Gromacs .itp files. In the ffcharmmnb.itp, the script gave the c6
> and c12, while the charmm's ffnonbond.itp showed  epsilon and sigma.I do not
> understand the relation between the  c6/c12 and epsilon and sigma, and I
> have a poor Perl skill. Can someone give me a solution?  In addition, the
> script makes all atoms' charge zero in the file, which is not the case in
> the ffnonbond.itp. Why is it?
> 
> Thank you!
> 
> Qing Liu
> 
> 
> 
> --
> View this message in context: 
> http://gromacs.5086.n6.nabble.com/The-problem-of-converting-CGenff-parameters-to-those-of-Gromacs-tp5002042.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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==
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Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Lennard-Jones Parameters

[Peter C. Lai]

On 2012-10-15 05:54:58AM -0400, Justin Lemkul wrote:
> 
> 
> On 10/15/12 5:45 AM, cuong nguyen wrote:
> > Dear,
> >
> > The top file downloaded from PRODRG did not consist of [atomtypes]. Please
> > tell me how can I add and use this function?
> >
> 
> I see no need to change anything about the L-J parameters.  Is there some 
> reason 
> you believe them to be incorrect?  If you modify L-J parameters, you're no 
> longer using Gromos96 43a1.  In PRODRG topologies, the charges and charge 
> groups 
> certainly need changing, but I have never seen a need to hack the L-J 
> parameters.
> 
> -Justin

I think he needs to go back and ask the authors of the paper he is trying to 
reproduce about how to parameterize 1-octanol according their specifications. 
If they are using different LJ for the atoms in this molecule from 43a1 then 
they are obviously not using gromos96 43a1 :)

> 
> > Best regards,
> >
> > Cuong
> >
> > On 15 October 2012 16:43, Peter C. Lai  wrote:
> >
> >> Is there no [atomtypes] section in the top file?
> >>
> >> On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote:
> >>> Thanks for you email.
> >>> I already had the .gro and .top files from PRODRG. Now I want to
> >> reproduce
> >>> these files following the LJ parameters in a published paper (charge,
> >> sigma
> >>> and epsilon values). I can change the charge in the top file, yet I do
> >> not
> >>> know how to change sigma and epsilon values.
> >>>
> >>> Best regards,
> >>>
> >>> Cuong
> >>>
> >>> On 15 October 2012 13:57, Peter C. Lai  wrote:
> >>>
> >>>> It's hard to understand your question. What do you mean by "reference
> >>>> parameters"? You said you already obtained a .gro and .top from PRODRG,
> >>>> which
> >>>> uses the gromos 43a1 forcefield to derive the parameters, so if you
> >> need
> >>>> to change the LJ parameters, edit the top file it gave you.
> >>>>
> >>>> If you want to reproduce the results of a published paper, you should
> >> use
> >>>> the
> >>>> forcefield and parameters specified in that paper and contact the
> >> author(s)
> >>>> if more details are needed.
> >>>>
> >>>> On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote:
> >>>>> Thank you very much for your email, Justin.
> >>>>> in case I want to use the reference parameters, which force-field and
> >>>> what
> >>>>> should I do to get the .gro and .top files for this molecule?
> >>>>>
> >>>>> Best regards,
> >>>>>
> >>>>> Cuong
> >>>>>
> >>>>>
> >>>>> On 12 October 2012 21:14, Justin Lemkul  wrote:
> >>>>>
> >>>>>>
> >>>>>>
> >>>>>> On 10/12/12 8:04 AM, cuong nguyen wrote:
> >>>>>>
> >>>>>>>Dear Gromacs Users,
> >>>>>>>
> >>>>>>> I got the .gro and .top files of 1-octanol downloaded from PRODRG
> >>>> website.
> >>>>>>> Please let me know if I can change charge, epsilon and sigma of
> >> the
> >>>>>>> molecule as written in a paper? and How to do?
> >>>>>>>
> >>>>>>>
> >>>>>> Atom types from PRODRG rarely, if ever, need changing.  Charges
> >> can be
> >>>>>> taken first by chemical homology (group-based approach that makes
> >>>> Gromos
> >>>>>> force fields convenient) and then by calculating the charges
> >> yourself.
> >>>>   For
> >>>>>> 1-octanol, it should be very straightforward to obtain parameters,
> >> zero
> >>>>>> charges on all the C atoms except for the one in the alocohol, then
> >>>>>> standard alcohol charges for the C-O-H.  Whether or not those
> >>>> parameters
> >>>>>> are sufficiently accurate is up to you to decide, but that's the
> >>>> approach
> >>>>>> one would take with this particular force field.
> >>>>>>
> >>>>>> -Justin
> >>>>>>
> >>>>>> --
> >>>>>> =

Re: [gmx-users] losing data in trjconv?

[Peter C. Lai]

Was traj.trr output by the same machine/mdrun as the machine you are running
trjconv on?

Is traj.trr (or the mdrun that wrote it) double precision and trjconv is 
compiled float (single precision)?

On 2012-10-15 02:31:00AM -0700, Gil Claudio wrote:
> Hi all,
> 
> When I do the following command
> 
> trjconv -f traj.trr -o traj_1.trr
> 
> the file size of traj_1.trr is around 25% smaller than traj.trr.
> 
> Does traj_1.trr contain less data than traj.trr?
> 
> Thanks
> 
> Gil
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-- 
======
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Lennard-Jones Parameters

[Peter C. Lai]

Is there no [atomtypes] section in the top file?

On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote:
> Thanks for you email.
> I already had the .gro and .top files from PRODRG. Now I want to reproduce
> these files following the LJ parameters in a published paper (charge, sigma
> and epsilon values). I can change the charge in the top file, yet I do not
> know how to change sigma and epsilon values.
> 
> Best regards,
> 
> Cuong
> 
> On 15 October 2012 13:57, Peter C. Lai  wrote:
> 
> > It's hard to understand your question. What do you mean by "reference
> > parameters"? You said you already obtained a .gro and .top from PRODRG,
> > which
> > uses the gromos 43a1 forcefield to derive the parameters, so if you need
> > to change the LJ parameters, edit the top file it gave you.
> >
> > If you want to reproduce the results of a published paper, you should use
> > the
> > forcefield and parameters specified in that paper and contact the author(s)
> > if more details are needed.
> >
> > On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote:
> > > Thank you very much for your email, Justin.
> > > in case I want to use the reference parameters, which force-field and
> > what
> > > should I do to get the .gro and .top files for this molecule?
> > >
> > > Best regards,
> > >
> > > Cuong
> > >
> > >
> > > On 12 October 2012 21:14, Justin Lemkul  wrote:
> > >
> > > >
> > > >
> > > > On 10/12/12 8:04 AM, cuong nguyen wrote:
> > > >
> > > >>   Dear Gromacs Users,
> > > >>
> > > >> I got the .gro and .top files of 1-octanol downloaded from PRODRG
> > website.
> > > >> Please let me know if I can change charge, epsilon and sigma of the
> > > >> molecule as written in a paper? and How to do?
> > > >>
> > > >>
> > > > Atom types from PRODRG rarely, if ever, need changing.  Charges can be
> > > > taken first by chemical homology (group-based approach that makes
> > Gromos
> > > > force fields convenient) and then by calculating the charges yourself.
> >  For
> > > > 1-octanol, it should be very straightforward to obtain parameters, zero
> > > > charges on all the C atoms except for the one in the alocohol, then
> > > > standard alcohol charges for the C-O-H.  Whether or not those
> > parameters
> > > > are sufficiently accurate is up to you to decide, but that's the
> > approach
> > > > one would take with this particular force field.
> > > >
> > > > -Justin
> > > >
> > > > --
> > > > ==**==
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Research Scientist
> > > > Department of Biochemistry
> > > > Virginia Tech
> > > > Blacksburg, VA
> > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > > >
> > > > ==**==
> > > > --
> > > > gmx-users mailing listgmx-users@gromacs.org
> > > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > > > * Please search the archive at http://www.gromacs.org/**
> > > > Support/Mailing_Lists/Search<
> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > > > * Please don't post (un)subscribe requests to the list. Use the www
> > > > interface or send it to gmx-users-requ...@gromacs.org.
> > > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> > http://www.gromacs.org/Support/Mailing_Lists>
> > > >
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
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> >
> > --
> > ==
> > Peter C. Lai| University o

Re: [gmx-users] Problem with equilibrated lipid bilayer structure

[Peter C. Lai]

On 2012-10-15 03:10:18PM +0800, Jernej Zidar wrote:
> The reason for using SPCE instead of TIP3P is that it performs  way
> better than TIP3P. This point is being emphasized everywhere along the
> documentation. I will try simulating using TIP3P model.
> >
> > Is there a reason to switch water models? Gromacs supports both the
> > traditional TIP3P and the CHARMM TIP3P (TIPS3P).
> >
> > Since you need to reinitialize velocities, it may not be a good idea to use
> > Nose-Hoover and Parinello-Rahman straight away. Furthermore, you need
> > to gen_vel=yes since gromacs has no velocity from your previous charmm run
> > and subjecting an otherwise frozen system to a parinello-rahman thermostat 
> > is
> > asking for trouble.
> 
> gen_vel=yes does not seem to help

Have you tried just doing NVT with tcoupl = V-rescale and tau_t = 0.1 0.1?

> 
> >
> > Also, pressure coupling for NPT should probably be semiisotropic for 
> > bilayers.
> > Finally you may want to experiment with EnerPres; see also
> > http://pubs.acs.org/doi/abs/10.1021/ct3003157 (although this isn't related 
> > to
> > your crash).
> 
> EnerPres is already set.
> 
>   I tried your suggestions but the simulation still fails.
> 
> Best,
> Jernej Zidar
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==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] VMD problem?

[Peter C. Lai]

Depending on the # of atoms, 6000 frames may exceed the amount of ram a 32bit
application can address (4GB). If you're having problems with the 64bit 
version, you should probably ask the vmd-l list.

The only workaround other than that is trjconv -skip and make a trajectory 
file that skips frames and will load under 4GB of ram.

On 2012-10-15 08:15:34AM +0200, Albert wrote:
> hello:
> 
>   I've installed gromacs in my macbookPro with 10.8 OS system. I am 
> trying to import gromacs trajectory which contains 6000 frames. However, 
> the VMD always clashed
> 
> 
> 
> VMD(552,0xac879a28) malloc: *** mmap(size=831488) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> libc++abi.dylib: terminate called throwing an exception
> /Applications/VMD 1.9.1.app/Contents/MacOS/startup.command: line 7:   
> 552 Abort trap: 6 "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
> logout
> 
> 
> 
> Does anybody have any idae how to solve this problem? I try to install 
> the 64bit VMD, but it crashed as soon as it start up.
> 
> thank you very much
> Albert
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==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] Problem with equilibrated lipid bilayer structure

[Peter C. Lai]

ompressibility = 4.5e-5  ; isothermal compressibility, bar^-1
> ; Periodic boundary conditions
> pbc   = xyz   ; 3-D PBC
> ; Dispersion correction
> DispCorr  = EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel   = no; Velocity generation is off
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the
> solvent/ions
> nstcomm = 1
> comm-mode   = Linear
> comm-grps   = LIPID SOL
> refcoord_scaling = all
> - - - -
> 
>   I imagine I'm doing something wrong but I'm unable to be able to
> pinpoint the error. I have also tried the NPT-simulated annealing path
> suggested in the GROMACS' protein-membrane tutorial but to no avail.
> I'm using the GROMACS version of the CHARMM36 lipid forcefield.
> 
> Thanks in advance for any advice,
> Jernej Zidar
> -- 
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==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Lennard-Jones Parameters

[Peter C. Lai]

It's hard to understand your question. What do you mean by "reference
parameters"? You said you already obtained a .gro and .top from PRODRG, which 
uses the gromos 43a1 forcefield to derive the parameters, so if you need
to change the LJ parameters, edit the top file it gave you.

If you want to reproduce the results of a published paper, you should use the 
forcefield and parameters specified in that paper and contact the author(s)
if more details are needed.

On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote:
> Thank you very much for your email, Justin.
> in case I want to use the reference parameters, which force-field and what
> should I do to get the .gro and .top files for this molecule?
> 
> Best regards,
> 
> Cuong
> 
> 
> On 12 October 2012 21:14, Justin Lemkul  wrote:
> 
> >
> >
> > On 10/12/12 8:04 AM, cuong nguyen wrote:
> >
> >>   Dear Gromacs Users,
> >>
> >> I got the .gro and .top files of 1-octanol downloaded from PRODRG website.
> >> Please let me know if I can change charge, epsilon and sigma of the
> >> molecule as written in a paper? and How to do?
> >>
> >>
> > Atom types from PRODRG rarely, if ever, need changing.  Charges can be
> > taken first by chemical homology (group-based approach that makes Gromos
> > force fields convenient) and then by calculating the charges yourself.  For
> > 1-octanol, it should be very straightforward to obtain parameters, zero
> > charges on all the C atoms except for the one in the alocohol, then
> > standard alcohol charges for the C-O-H.  Whether or not those parameters
> > are sufficiently accurate is up to you to decide, but that's the approach
> > one would take with this particular force field.
> >
> > -Justin
> >
> > --
> > ==**==
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >
> > ==**==
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
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> >  posting!
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> >
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==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] Re: small tc-group

[Peter C. Lai]

On 2012-10-12 04:40:35AM -0700, fciocco wrote:
> Thanks Peter for your reply
> 
> actually, I did not think about that possibility because in the most
> windows, I have this small highly charged peptide out of the membrane.
> Moreover, in the last US windows, the peptide creates a defect and there are
> several water molecules inside the membrane. So, if I think about this fact,
> I associate the peptide with the SOL molecules, because of it charged
> nature...
>  
> some questions come to my mind:
> 
> If I'll have a simple charged aminoacid or a bigger charged peptide, the
> definition for the tc_groups that you proposed me, would be the same (i.e.
> peptide_membrane)? I think that it could be a little tricky to see. 
> 

Yeah this will be size dependent. I went back and looked at Justin's 
KALP_15 tutorial and he appears to be able to run a separate tc-group
for a single continuous peptide of 15 residues.

My area of familiarity is with continuous membrane proteins averaging 
300-400 amino acids, and I use separate tc-groups for protein, membrane, and 
SOL_Ions. However, when I introduce small molecule ligands into the system, 
which are on the order of 10-15 heavy atoms per molecule, they are temperature 
coupled with water because: they are still much smaller than lipid acyl 
chains and there are very few of them compared to the number of water 
molecules in the system (never more than 1:200 ratio) so they do not 
contribute too much to sampling or distribution. If you are concerned 
about temperature coupling very small peptides or single AAs then try 
coupling them to water and see what happens. 

> I should be worried about the high temperature fluctuations if I choose the
> peptide as an individual tc_group.?
> 
> Can this different elections of the tc_grps affect the final PMF profile?  
> 

If you have significant temperature fluctuations they will, by definition...

-- 
==========
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] small tc-group

[Peter C. Lai]

I would couple it with the membrane to be honest. The point of the different
groups is to avoid the hot solvent cold solute sitution. Molecules with 
similar degrees of freedom have comparable heat capacities. Your small 
peptide is closer in size and bond layout to a lipid chain than to water.
The end state of the system also hase the peptide physically coupled to the
bilayer too, so Membrane_Peptide seems to be most consistent approach. 

On 2012-10-11 07:23:26PM -0700, fciocco wrote:
> Hi
> 
> I have a system with a lipid bilayer (128 phospolipids), aproximately 30 SOL
> molecules per lipid, and a small highly charged peptide at certain distance
> from the bilayer. I want to do a pulling simulation in order to pull the
> peptide inside the membrane along the z-direction. So, taking into account
> that I want to explore the differents configurations doing a serie of US
> simulations, and that in some windows I have the peptide in the water bulk
> and in others it is inside the hydrophobic core of the membrane (but with
> some hydration water molecules), I'm wondering about what is the best
> approach for define the tc-groups..?
> Peptide Membrane SOL_Ions or Membrane Peptide_SOL_Ions ?
>  
> Note: when I choose the peptide separately, the temperature fluctuations are
> high (between 50 and 100K approximately).  
> 
> any comment would be very appreciated.
> 
> best regards, Facundo 
> 
> 
> 
> --
> View this message in context: 
> http://gromacs.5086.n6.nabble.com/small-tc-group-tp5001927.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Model of water

[Peter C. Lai]

I used TIPS3P in everything, because after all, it's CHARMM's water and
no reviewer can complain about using it with CHARMM. If you want a faster 
simulation you can try using the regular TIP3P and see if the bilayer metrics 
remain satisfactory for you. If you still have doubts, run simulations with 
both TIPS3P and TIP3P and decide if the differences are significant. IIRC 
Thomas Piggot's latest CHARMM36 Gromacs paper "Molecular Dynamics Simulations 
of Phosphatidylcholine Membranes: A Comparative Force Field Study" has some 
results on POPC in TIP3P vs. TIPS3P.

When using genbox, you always use spc216.gro as the starting solvent 
coordinates. The waters will adopt the correct physical properties specified 
by the model and forcefield during equilibration.

On 2012-10-06 02:40:58AM -0700, Shima Arasteh wrote:
> As I studied in " Beyond modeling" by Peter Lai and coworkers, TIPS3P is the 
> CHARMM variant of TIP3P, which TIPS3P recognizes additional van der waals 
> interactions. So I guess I can use tips3p model of water instead of tip3p and 
> go on. Correct? 
> 
> Then I need to know which model of water should be used in later simulations 
> ( protein insertion in POPC) ? Is tips3p recommended?  
> 
> I'd like to know more about tips3p model. 
> 
> Thanks in advance.
> 
>  
> Sincerely,
> Shima
> 
> 
> - Original Message -
> From: Shima Arasteh 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Cc: 
> Sent: Saturday, October 6, 2012 11:54 AM
> Subject: Re: [gmx-users] Model of water
> 
> 
> 
> I tried to use genbox, but there is not tip3p.gro in GROMACS package, so 
> spc216.gro is recommended to be used. I want to know what exactly I need to 
> do to get the popc in water with tip3p model of water?
> 
> Thanks in advance.
> 
> Sincerely,
> Shima
> 
> 
> - Original Message -
> From: Shima Arasteh 
> To: Discussion list for GROMACS users 
> Cc: 
> Sent: Saturday, October 6, 2012 11:28 AM
> Subject: [gmx-users] Model of water
> 
> 
> 
>  Dears, 
> 
> I got a link sent me by Peter Lai to simulate POPC in water: 
> http://uab.hyperfine.info/~pcl/files/popc36/
> He used TIP3SP, as it is apparent in its top file. I want to use simulate my 
> own system of POPC in water with tip3p model of water? Is it possible to use 
> its Peter's top and itp files? 
> 
> Please help me
> 
> Sincerely,
> Shima
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Temperature in simulation

[Peter C. Lai]

It sounds like you want to report that you created a bilayer, equilibrated it
at 310K then inserted the protein and ran MD of the embedded system at 300K?

On 2012-10-03 06:57:22AM -0700, Shima Arasteh wrote:
> I see that the velocities will be reassigned, but what I'm concerned about, 
> is reporting the results in a paper. How would it be?
> 
> Thanks for your suggestion Peter.
> 
>  
> Sincerely,
> Shima
> 
> 
> - Original Message -
> From: Peter C. Lai 
> To: Discussion list for GROMACS users 
> Cc: 
> Sent: Wednesday, October 3, 2012 5:16 PM
> Subject: Re: [gmx-users] Temperature in simulation
> 
> You should do NVT equilibration to your target temperature. Your system is
> already heavily changed between the equilibrated full bilayer and the 
> embedded protein system so velocities will be reassigned anyway.
> 
> On 2012-10-03 06:39:39AM -0700, Shima Arasteh wrote:
> > 
> > 
> > Hi all,
> > 
> > I want to insert a protein in POPC lipid bilayer. 
> > 
> > First of all, I simulated POPC in water in 310 K. Now, I want to insert 
> > protein in lipid-water. To simulate protein-lipid-water system I want to 
> > run NVT in 300 K and then go on. Does anybody know it would be  incorrect 
> > logically ? 
> > 
> > 
> > As I know, 10 degree increase in temperature of system, may result in some 
> > troubles in my small protein. But I guess this would not happen for lipid 
> > bilayer.
> > 
> > 
> > Thanks in advance for your suggestions.
> > 
> > 
> > Sincerely,
> > Shima 
> > -- 
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> -- 
> ==
> Peter C. Lai            | University of Alabama-Birmingham
> Programmer/Analyst        | KAUL 752A
> Genetics, Div. of Research    | 705 South 20th Street
> p...@uab.edu            | Birmingham AL 35294-4461
> (205) 690-0808            |
> ==
> 
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Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Temperature in simulation

[Peter C. Lai]

You should do NVT equilibration to your target temperature. Your system is
already heavily changed between the equilibrated full bilayer and the 
embedded protein system so velocities will be reassigned anyway.

On 2012-10-03 06:39:39AM -0700, Shima Arasteh wrote:
> 
> 
> Hi all,
> 
> I want to insert a protein in POPC lipid bilayer. 
> 
> First of all, I simulated POPC in water in 310 K. Now, I want to insert 
> protein in lipid-water. To simulate protein-lipid-water system I want to run 
> NVT in 300 K and then go on. Does anybody know it would be  incorrect 
> logically ? 
> 
> 
> As I know, 10 degree increase in temperature of system, may result in some 
> troubles in my small protein. But I guess this would not happen for lipid 
> bilayer.
> 
> 
> Thanks in advance for your suggestions.
> 
> 
> Sincerely,
> Shima 
> -- 
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==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Ion conduction through a protein-membrane system

[Peter C. Lai]

On 2012-10-01 11:16:43PM -0700, Shima Arasteh wrote:
> 
> 
>  Dear users,
> 
> I want to study ion conduction through a protein-memrane system. 
> First of all, I tried to simulate a usual protein-membrane system. I'd like 
> to know if it is possible to add asymmetrical number of ions to leaflets of 
> membrane?

Yes. You need to first use trjorder -z to reorder the waters, then you need 
to make 2 index group of consecutive atoms in each layer. Tell genion to only 
pick waters from the separate index groups. It is important that the index
groups representing the water surrounding the "top" and "bottom" leaflet are 
consecutive in atom number or else genion will refuse to run. The easiest way 
to do that is to find Z around the middle of the bilayer where there are 
no waters and separate the top waters from the bottom waters. 

Note that use of pbc=xyz Periodic Boundary Conditions will allow the 
"extracellular" ions to travel into the "intracellular" space as the top ions 
diffuse +Z (and the "intracellular" ions can diffuse -Z into the 
"extracellular" space), so track your ion movements appropriately.

Finally if the total charge of the system isn't balanced, grompp will throw
a notice or a warning. I don't know what the consequences of running a 
simulation of a non-neutral system has on things like energy conservation...

> Secondly, is it possible to  apply an external electrical field to study ion 
> conduction in a system?
> 

The manual appears suggests such a thing might be possible to some extent.
You'll probably want to look for yourself to see if your use-case is supported.

-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] pdb2gmx with more than 9999 residues

[Peter C. Lai]

A pdb file with a resid >  exceeds the proper PDB format.

You can resolvate a dry lipid bilayer using genbox fine; I don't know what 
problem you have with the solvation and minimization using that method,
http://manual.gromacs.org/current/online/genbox.html

You can also pdb2gmx or editconf the lipids and water separately as you 
suggested, then merge the files and run ediconf on the merged file to 
renumber the atoms.

On 2012-10-02 02:16:00PM +0800, Jernej Zidar wrote:
> Hi.
>   I'm trying to import a solvated lipid bilayer
> (cholesterol+POPC+water) I generated in CHARMM but I have a problem
> with pdb2gmx unwilling to accept the segment containing water
> molecules. It does import everything seemingly correctly, yet when one
> examines the resulting .gro file, he can see that the system does not
> accept more than  residues/segment: residue 1 becomes 1000 and
> so on.
> 
>   Now, what can one do ammend the current situation?
> 
>   One option would be to import only the lipid part of the system and
> then solvate it again in GROMACS, but that path is not really useful
> because it doesn't allow to fine tune the amount and location of water
> molecules. I tried this option but it doesn't work in my case as
> there's a gaping hole between the water layer and the lipids, that
> cause the minimization to essentially fail.
> 
>   Another option would be to import the lipid and water part
> separately but this would again cause problems with atom numbering
> when both segments would be combined together.
> 
>   Manually editing the PDB file is not an option as the PDB file has
> ~80.000 lines.
> 
>   Any other way?
> 
>   I'm using GROMACS 4.5.5 on Ubuntu 12.04 64-bit.
> 
> Thanks in advance,
> Jernej
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==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] a question related to grompp command

[Peter C. Lai]

On 2012-09-29 12:42:29AM -0700, Acoot Brett wrote:
> Dear All,
> 
> I just run a grompp command "grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p 
> topol.top -o npt.tpr". It gives the following message,
> 
> Generated 2211 of the 2211 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2211 of the 2211 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'CL'
> 
> Will you please tell me why grompp "exclude" and "turning"? What are their 
> functions? Based on what grompp process "exclude" and "turning"?
> 
> I am looking forward to getting your reply.

Turning refers to turning bonds into constraints are defined in the .mdp file:

constraints = whatever you have defined here (probably all-bonds if grompp
is reporting that all bonds are turned into constraints)

neighbor exclusions are from the beginning of the topology file for that 
particular [ moleculetype ] in the nrexcl field

[ moleculetype ]
; name  nrexcl
Protein_chain_A 3

nonbonded interactions between atoms that are no further than nrexcl bonds 
away are excluded. See also
http://lists.gromacs.org/pipermail/gmx-users/2011-May/061072.html

-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] Assignment of new velocities for multi-runs

[Peter C. Lai]

If the system is already well equilibrated previously then you can probably 
safely reassign velocities during NPT. The best way to do this would probably
be to take the equilibrated checkpoint file as the starting point:

grompp -f genvel-yes-npt.mdp -t previous.cpt ...

You'll still have to wait some ns for the system to reequilibrate so data
comparisons between the runs for the first several ns will not be meaningful,
so ultimately, the question is what you do you hope to gain from reassigning
velocities at the beginning?

On 2012-09-28 11:59:02PM -0700, James Starlight wrote:
> Dear All!
> 
> I'd like to perform several simulations of the membrane protein
> started from the common conditions which differs only in the initial
> velocities ( for each simulation random speed distribution will be
> used from the Maxwell distribution).
> 
> Because I simulate membrane protein the long equilibration phase is
> required for that system. I've noticed that new velocities sets are
> assigned in the NVT phase of equilibration (100ps) after which more
> prolongest npt equilibration (10ns) is followed.
> 
> Does it require that new velocities always be assigned exactly during
> equilibration of my system ? Could I use new velocities in the
> production md run instead ? In the latter case my system will be
> equilibrated with one velocities but further production MD will be
> with another velocities each time? (so in latter case I can avoid long
> equilibration phase for each simulation).
> 
> 
> James
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==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] Do not want to add hydrogens to intial pdb structure

[Peter C. Lai]

Specify a united atom forcefield?

You can also do a direct conversion from pdb to gro using editconf, but
that's not going to generate a topology.

On 2012-09-27 03:38:15PM +0530, mohan maruthi sena wrote:
> Hi all,
>  When we generate .gro , .top files  using pdb2gmx command it
> add hydrogens to the structure depending upon the valency of the atom. Is
> there any option in gromacs such that it does not add hydrogens to the
> intial structure .
> 
> 
> Thank you,
> Mohan
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-- 
==========
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] Installation in a SGI Cluster

[Peter C. Lai]

Check to see if the MPICC and MPI_HOME environment variables are set 
correctly to configure (it can't find mpicc).

On 2012-09-25 12:06:14PM -0300, Diego Nolasco wrote:
> Hello GROMACS users,
> 
> I am facing some problems to configure the gromacs installation in a x86_64
> GNU/Linux SGI Cluster XE with Suse.
> I am using ./configure --enable-mpi --without-x --disable-float and the
> error comes as below:
> 
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... /bin/mkdir -p
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking how to create a ustar tar archive... gnutar
> checking for cc... cc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether cc accepts -g... yes
> checking for cc option to accept ISO C89... none needed
> checking for style of include used by make... GNU
> checking dependency style of cc... gcc3
> checking dependency style of cc... gcc3
> checking for mpxlc... no
> checking for mpicc... no
> checking for mpcc... no
> checking for hcc... no
> checking whether the MPI cc command works... configure: error: Cannot
> compile and link MPI code with cc
> 
> I would really appreciate if someone assist me in this regard.
> Thank's in advance,
> 
> Diego Nolasco.
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==
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Programmer/Analyst  | KAUL 752A
Genetics Div. of Research   | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] Water molecule can not be settled - mdrun error

[Peter C. Lai]

On 2012-09-24 12:34:53PM -0400, Justin Lemkul wrote:
> 
> 
> On 9/24/12 12:31 PM, Peter C. Lai wrote:
> > As I noted before, you can safely ignore the gromacs notices when setting
> > them to the correct cutoffs I listed.
> >
> 
> Agreed.  Please use the cutoffs that have been posted explicitly 3-4 times 
> now.
> 
> > Your energy minimization still looks a bit high (1000)...
> >
> > Justin might have some more ideas...
> >
> 
> The maximum force is too high.  If this condition persists with the proper 
> cutoffs, then the topology is to blame.  You've yet to explain where the 
> parameters for lumiflavin came from, but if forces are high and the 
> simulations 
> collapse, then the parameterization is likely insufficiently accurate.

I was going to suggest running a minimization in double-precision just to 
check...

> > On 2012-09-24 05:07:59PM +0100, Lara Bunte wrote:
> >> Hi
> >>
> >> The result of the energy minimization before is:
> >>
> >> Steepest Descents:
> >> Tolerance (Fmax)   =  1.0e+03
> >> Number of steps= 5000
> >>
> >> Stepsize too small, or no change in energy.
> >> Converged to machine precision,
> >> but not to the requested precision Fmax < 1000
> >>
> >> Double precision normally gives you higher accuracy.
> >> You might need to increase your constraint accuracy, or turn
> >> off constraints alltogether (set constraints = none in mdp file)
> >>
> >> writing lowest energy coordinates.
> >>
> >> Steepest Descents converged to machine precision in 226 steps,
> >> but did not reach the requested Fmax < 1000.
> >> Potential Energy  = -1.3277053e+05
> >> Maximum force =  1.7070897e+03 on atom 8
> >> Norm of force =  3.8431282e+01
> >>
> >> My System is lumiflavin in water, tip3p water model and charmm27 force 
> >> field. My actual goal is to equilibrate the water around the lumiflavin 
> >> with that .mdp file I wrote. What is now wrong with the cut-offs? If I use 
> >> the settings for charmm27 cut-offs you wrote I got all that problems I 
> >> wrote. Would you please change here how it should look like:
> >>
> >>> define  = -DPOSRES
> >>>
> >>> integrator  = md
> >>> dt  = 0.002
> >>> emtol   = 1000.0
> >>> emstep  = 0.01
> >>> nsteps  = 5000
> >>>
> >>> nstlist = 1
> >>> rlist   = 1.5
> >>> rlistlong   = 1.4
> >>> rcoulomb= 1.5
> >>> coulombtype = pme
> >>> vdw-type= switch
> >>> rvdw_switch = 0.8
> >>> rvdw= 1.5
> >>>
> >>> nstxout = 100
> >>> nstvout = 100
> >>> nstenergy   = 100
> >>> nstlog  = 100
> >>>
> >>> tcoupl  = V-rescale
> >>> tc-grps = ISO SOL
> >>> tau_t   = 0.1   0.1
> >>> ref_t   = 300   300
> >>>
> >>> pcoupl  = no
> >>
> >> I am totaly frustrated and shortly for giving it up :-(:-( :-(
> >>
> >> Best greetings
> >> Lara
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> - Ursprüngliche Message -
> >> Von: Peter C. Lai 
> >> An: Lara Bunte 
> >> CC: "gmx-users@gromacs.org" 
> >> Gesendet: 17:57 Montag, 24.September 2012
> >> Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
> >>
> >> Then yes, your cutoffs are still wrong. However check to see if atom 8376 
> >> is
> >> clashing with something nearby (protein?). You also never gave any data 
> >> about
> >> the result of the previous energy minimization steps...
> >>
> >> On 2012-09-24 04:54:13PM +0100, Lara Bunte wrote:
> >>> Hi Peter
> >>>
> >>> My complete .mdp file is now:
> >>>
> >>> define  = -DPOSRES
> >>>
> >>> integrator  = md
> >>> dt  = 0.002
> >>> emtol   = 1000.0
> >>> emstep  = 0.01
> >>> nsteps  = 5000
> >>>
> >>> nstlist = 1
> >>> rlist   = 1.5
> >>> rlistlong

Re: [gmx-users] Water molecule can not be settled - mdrun error

[Peter C. Lai]

As I noted before, you can safely ignore the gromacs notices when setting
them to the correct cutoffs I listed.

Your energy minimization still looks a bit high (1000)...

Justin might have some more ideas...

On 2012-09-24 05:07:59PM +0100, Lara Bunte wrote:
> Hi
> 
> The result of the energy minimization before is:
> 
> Steepest Descents:
>    Tolerance (Fmax)   =  1.0e+03
>    Number of steps    = 5000
> 
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
> 
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> 
> writing lowest energy coordinates.
> 
> Steepest Descents converged to machine precision in 226 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -1.3277053e+05
> Maximum force =  1.7070897e+03 on atom 8
> Norm of force =  3.8431282e+01
> 
> My System is lumiflavin in water, tip3p water model and charmm27 force field. 
> My actual goal is to equilibrate the water around the lumiflavin with that 
> .mdp file I wrote. What is now wrong with the cut-offs? If I use the settings 
> for charmm27 cut-offs you wrote I got all that problems I wrote. Would you 
> please change here how it should look like:
> 
> > define  = -DPOSRES
> > 
> > integrator  = md
> > dt  = 0.002
> > emtol   = 1000.0    
> > emstep  = 0.01  
> > nsteps  = 5000  
> > 
> > nstlist = 1 
> > rlist   = 1.5    
> > rlistlong   = 1.4   
> > rcoulomb    = 1.5   
> > coulombtype = pme
> > vdw-type    = switch
> > rvdw_switch = 0.8
> > rvdw    = 1.5   
> > 
> > nstxout = 100   
> > nstvout = 100   
> > nstenergy   = 100   
> > nstlog  = 100   
> > 
> > tcoupl  = V-rescale 
> > tc-grps = ISO SOL   
> > tau_t   = 0.1   0.1     
> > ref_t   = 300   300 
> > 
> > pcoupl  = no
> 
> I am totaly frustrated and shortly for giving it up :-(:-( :-(
> 
> Best greetings
> Lara
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> - Ursprüngliche Message -
> Von: Peter C. Lai 
> An: Lara Bunte 
> CC: "gmx-users@gromacs.org" 
> Gesendet: 17:57 Montag, 24.September 2012
> Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
> 
> Then yes, your cutoffs are still wrong. However check to see if atom 8376 is
> clashing with something nearby (protein?). You also never gave any data about
> the result of the previous energy minimization steps...
> 
> On 2012-09-24 04:54:13PM +0100, Lara Bunte wrote:
> > Hi Peter
> > 
> > My complete .mdp file is now:
> > 
> > define  = -DPOSRES
> > 
> > integrator  = md
> > dt  = 0.002
> > emtol   = 1000.0    
> > emstep  = 0.01  
> > nsteps  = 5000  
> > 
> > nstlist = 1 
> > rlist   = 1.5    
> > rlistlong   = 1.4   
> > rcoulomb    = 1.5   
> > coulombtype = pme
> > vdw-type    = switch
> > rvdw_switch = 0.8
> > rvdw        = 1.5   
> > 
> > nstxout = 100   
> > nstvout = 100   
> > nstenergy   = 100   
> > nstlog  = 100   
> > 
> > tcoupl  = V-rescale 
> > tc-grps = ISO SOL   
> > tau_t   = 0.1   0.1 
> > ref_t   = 300   300 
> > 
> > pcoupl  = no
> > 
> > Greetings
> > Lara
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > - Ursprüngliche Message -
> > Von: Peter C. Lai 
> > An: Lara Bunte 
> > CC: "gmx-users@gromacs.org" 
> > Gesendet: 17:46 Montag, 24.September 2012
> > Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
> > 
> > Is this energy minimization or actual integrator = md?
> > 
> > On 2012-09-24 04:44:18PM +0100, Lara Bunte wrote:
> > > Hello
> > > 
> > > Okay, I changed it to
> > > 
> > > nstlist         = 1
> > > rlist   = 1.5
> > > rlistlong   = 1.4
> >

Re: [gmx-users] About mdrun -nt number

[Peter C. Lai]

yes. but by default mdrun should allocate all 24. (that's what -nt 0 does,
allocate the maximum).

On 2012-09-24 05:01:11PM +0100, Lara Bunte wrote:
> If I have 24 processors in the machine, I could use mdrun -nt 24 for a high 
> performance?
> 
> Greetings
> Lara
> 
> 
> 
> 
> 
> ----- Ursprüngliche Message -
> Von: Peter C. Lai 
> An: Lara Bunte ; Discussion list for GROMACS users 
> 
> CC: 
> Gesendet: 17:58 Montag, 24.September 2012
> Betreff: Re: [gmx-users] About mdrun -nt number
> 
> A thread is like a process. (Except not all threads have to be processes,
> since that is an OS feature).
> 
> On 2012-09-24 04:55:20PM +0100, Lara Bunte wrote:
> > Sadly I don't know what a thread is. :( Sorry but I don't understand.
> > 
> > Greetings
> > Lara
> > 
> > 
> > 
> > 
> > 
> > - Ursprüngliche Message -
> > Von: Peter C. Lai 
> > An: Discussion list for GROMACS users 
> > CC: 
> > Gesendet: 17:43 Montag, 24.September 2012
> > Betreff: Re: [gmx-users] About mdrun -nt number
> > 
> > # of mdrun threads
> > 
> > -nt N is used to basically tell mdrun how many threads to spawn on the 
> > local host. We refer to threads since on some architectures, a single core
> > can handle multiple threads. (like 2 threads per core with hyperthreading).
> > 
> > On 2012-09-24 04:33:19PM +0100, Lara Bunte wrote:
> > > Hi
> > > 
> > > In the man page of mdrun is written for the option -nt int: "Number of 
> > > threads to start (0 is guess)"
> > > 
> > > What do this mean? What is a thread in this context?
> > > 
> > > Thanks
> > > Greetings
> > > Lara
> > > 
> > > -- 
> > > gmx-users mailing list    gmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at 
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the 
> > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > 
> > -- 
> > ==
> > Peter C. Lai            | University of Alabama-Birmingham
> > Programmer/Analyst        | KAUL 752A
> > Genetics, Div. of Research    | 705 South 20th Street
> > p...@uab.edu            | Birmingham AL 35294-4461
> > (205) 690-0808            |
> > ==
> > 
> > -- 
> > gmx-users mailing list    gmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at 
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > 
> > -- 
> > gmx-users mailing list    gmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at 
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> -- 
> ==
> Peter C. Lai            | University of Alabama-Birmingham
> Programmer/Analyst        | KAUL 752A
> Genetics, Div. of Research    | 705 South 20th Street
> p...@uab.edu            | Birmingham AL 35294-4461
> (205) 690-0808            |
> ==

-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] About mdrun -nt number

[Peter C. Lai]

A thread is like a process. (Except not all threads have to be processes,
since that is an OS feature).

On 2012-09-24 04:55:20PM +0100, Lara Bunte wrote:
> Sadly I don't know what a thread is. :( Sorry but I don't understand.
> 
> Greetings
> Lara
> 
> 
> 
> 
> 
> - Ursprüngliche Message -
> Von: Peter C. Lai 
> An: Discussion list for GROMACS users 
> CC: 
> Gesendet: 17:43 Montag, 24.September 2012
> Betreff: Re: [gmx-users] About mdrun -nt number
> 
> # of mdrun threads
> 
> -nt N is used to basically tell mdrun how many threads to spawn on the 
> local host. We refer to threads since on some architectures, a single core
> can handle multiple threads. (like 2 threads per core with hyperthreading).
> 
> On 2012-09-24 04:33:19PM +0100, Lara Bunte wrote:
> > Hi
> > 
> > In the man page of mdrun is written for the option -nt int: "Number of 
> > threads to start (0 is guess)"
> > 
> > What do this mean? What is a thread in this context?
> > 
> > Thanks
> > Greetings
> > Lara
> > 
> > -- 
> > gmx-users mailing list    gmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at 
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> -- 
> ==
> Peter C. Lai            | University of Alabama-Birmingham
> Programmer/Analyst        | KAUL 752A
> Genetics, Div. of Research    | 705 South 20th Street
> p...@uab.edu            | Birmingham AL 35294-4461
> (205) 690-0808            |
> ==
> 
> -- 
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] Water molecule can not be settled - mdrun error

[Peter C. Lai]

Then yes, your cutoffs are still wrong. However check to see if atom 8376 is
clashing with something nearby (protein?). You also never gave any data about
the result of the previous energy minimization steps...

On 2012-09-24 04:54:13PM +0100, Lara Bunte wrote:
> Hi Peter
> 
> My complete .mdp file is now:
> 
> define  = -DPOSRES
> 
> integrator  = md
> dt  = 0.002
> emtol   = 1000.0    
> emstep  = 0.01  
> nsteps  = 5000  
> 
> nstlist = 1 
> rlist   = 1.5    
> rlistlong   = 1.4   
> rcoulomb    = 1.5   
> coulombtype = pme
> vdw-type    = switch
> rvdw_switch = 0.8
> rvdw    = 1.5   
> 
> nstxout = 100   
> nstvout = 100   
> nstenergy   = 100   
> nstlog  = 100   
> 
> tcoupl  = V-rescale 
> tc-grps = ISO SOL   
> tau_t   = 0.1   0.1 
> ref_t   = 300   300 
> 
> pcoupl  = no
> 
> Greetings
> Lara
> 
> 
> 
> 
> 
> 
> 
> - Ursprüngliche Message -
> Von: Peter C. Lai 
> An: Lara Bunte 
> CC: "gmx-users@gromacs.org" 
> Gesendet: 17:46 Montag, 24.September 2012
> Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
> 
> Is this energy minimization or actual integrator = md?
> 
> On 2012-09-24 04:44:18PM +0100, Lara Bunte wrote:
> > Hello
> > 
> > Okay, I changed it to
> > 
> > nstlist = 1
> > rlist   = 1.5
> > rlistlong   = 1.4
> > rcoulomb    = 1.5
> > coulombtype = pme
> > vdw-type    = switch
> > rvdw_switch = 0.8
> > rvdw    = 1.5
> > 
> > in my .mdp file and I got now this error:
> > 
> > step 1352: Water molecule starting at atom 8376 can not be settled.
> > Check for bad contacts and/or reduce the timestep if appropriate.
> > Wrote pdb files with previous and current coordinates
> > 
> > Are the .mdp Options still a problem?
> > 
> > 
> > I am really thankful for the big amount of help. Thank you.
> > Lara
> > 
> > 
> > 
> > 
> > 
> > 
> > - Ursprüngliche Message -
> > Von: Peter C. Lai 
> > An: Discussion list for GROMACS users 
> > CC: Lara Bunte 
> > Gesendet: 22:13 Freitag, 21.September 2012
> > Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
> > 
> > On 2012-09-21 02:59:17PM -0400, Justin Lemkul wrote:
> > > 
> > > 
> > > On 9/21/12 1:31 PM, Lara Bunte wrote:
> > > > Hi Justin
> > > >
> > > > I used this settings except of vdw-type = switch and rvdw_switch = 0.8 
> > > > and with this settings grompp gives me two notes and one of this notes 
> > > > is inconsistent:
> > > >
> > > > NOTE 1 [file pr.mdp]:
> > > >    For energy conservation with switch/shift potentials, rlist should 
> > > >be 0.1
> > > >    to 0.3 nm larger than rvdw.
> > > >
> > > > Because I thought rlist hast to be 1.2 and rvdw hast to be 1.2 for my 
> > > > CHARMM27 force field.
> > > >
> > > >
> > > 
> > > Increase rlist as suggested to accommodate the algorithm.  Since CHARMM 
> > > does not 
> > > use charge groups (well, it uses single-atom charge groups) this isn't 
> > > such a 
> > > big deal.  For a force field like Gromos96, it matters a lot more.
> > 
> > Actually rlist has to be equal to rvdw for this case (PME will complain if 
> > it
> > doesn't). I haven't had a water settling issue in a correctly setup system
> > with rlist = rvdw and a switched rvdw.  I do remember a bug in the code that
> > forgets rlistlong is specified.
> > 
> > > 
> > > >
> > > > My second note is:
> > > >
> > > > NOTE 2 [file pr.mdp]:
> > > >    The sum of the two largest charge group radii (0.079505) is larger 
> > > >than
> > > >    rlist (1.20) - rvdw (1.20)
> > > >
> > > >
> > > > which I sadly don't understand.
> > > >
> > > 
> > > http://www.gromacs.org/Documentation/Errors?highlight=errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
> > > 
> > > -Justin
> > > 
> > 
> > I also get this note too, but th

Re: [gmx-users] Water molecule can not be settled - mdrun error

[Peter C. Lai]

Is this energy minimization or actual integrator = md?

On 2012-09-24 04:44:18PM +0100, Lara Bunte wrote:
> Hello
> 
> Okay, I changed it to
> 
> nstlist = 1
> rlist   = 1.5
> rlistlong   = 1.4
> rcoulomb    = 1.5
> coulombtype = pme
> vdw-type    = switch
> rvdw_switch = 0.8
> rvdw    = 1.5
> 
> in my .mdp file and I got now this error:
> 
> step 1352: Water molecule starting at atom 8376 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> 
> Are the .mdp Options still a problem?
> 
> 
> I am really thankful for the big amount of help. Thank you.
> Lara
> 
> 
> 
> 
> 
> 
> - Ursprüngliche Message -
> Von: Peter C. Lai 
> An: Discussion list for GROMACS users 
> CC: Lara Bunte 
> Gesendet: 22:13 Freitag, 21.September 2012
> Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error
> 
> On 2012-09-21 02:59:17PM -0400, Justin Lemkul wrote:
> > 
> > 
> > On 9/21/12 1:31 PM, Lara Bunte wrote:
> > > Hi Justin
> > >
> > > I used this settings except of vdw-type = switch and rvdw_switch = 0.8 
> > > and with this settings grompp gives me two notes and one of this notes is 
> > > inconsistent:
> > >
> > > NOTE 1 [file pr.mdp]:
> > >    For energy conservation with switch/shift potentials, rlist should be 
> > >0.1
> > >    to 0.3 nm larger than rvdw.
> > >
> > > Because I thought rlist hast to be 1.2 and rvdw hast to be 1.2 for my 
> > > CHARMM27 force field.
> > >
> > >
> > 
> > Increase rlist as suggested to accommodate the algorithm.  Since CHARMM 
> > does not 
> > use charge groups (well, it uses single-atom charge groups) this isn't such 
> > a 
> > big deal.  For a force field like Gromos96, it matters a lot more.
> 
> Actually rlist has to be equal to rvdw for this case (PME will complain if it
> doesn't). I haven't had a water settling issue in a correctly setup system
> with rlist = rvdw and a switched rvdw.  I do remember a bug in the code that
> forgets rlistlong is specified.
> 
> > 
> > >
> > > My second note is:
> > >
> > > NOTE 2 [file pr.mdp]:
> > >    The sum of the two largest charge group radii (0.079505) is larger than
> > >    rlist (1.20) - rvdw (1.20)
> > >
> > >
> > > which I sadly don't understand.
> > >
> > 
> > http://www.gromacs.org/Documentation/Errors?highlight=errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
> > 
> > -Justin
> > 
> 
> I also get this note too, but the sum looks fine to me. If the sum > 0.15 then
> it typically indicates chargegroups are being used, which they shouldn't for 
> charmm-based forcefields, but in this case the distance shown is on the order
> of a heavy-h bond. I think the note message is still related to rlist vs. 
> rlistlong.
> 
> anyway, I routinely ignore both these notes and it hasn't given me problems
> so far. I would still go bck to check the specific water that could not settle
> and see what the other particles near it are since that is probably the root
> of the problem. Also, we haven't been told what the results of the energy 
> minimzation was...
> 
> -- 
> ==
> Peter C. Lai            | University of Alabama-Birmingham
> Programmer/Analyst        | KAUL 752A
> Genetics, Div. of Research    | 705 South 20th Street
> p...@uab.edu            | Birmingham AL 35294-4461
> (205) 690-0808            |
> ==

-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] About mdrun -nt number

[Peter C. Lai]

# of mdrun threads

-nt N is used to basically tell mdrun how many threads to spawn on the 
local host. We refer to threads since on some architectures, a single core
can handle multiple threads. (like 2 threads per core with hyperthreading).

On 2012-09-24 04:33:19PM +0100, Lara Bunte wrote:
> Hi
> 
> In the man page of mdrun is written for the option -nt int: "Number of 
> threads to start (0 is guess)"
> 
> What do this mean? What is a thread in this context?
> 
> Thanks
> Greetings
> Lara
> 
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Re: [gmx-users] packing lipids

[Peter C. Lai]

What does trace show? (Trace is supposed to draw a vertex between each
alpha carbon). VMD has no knowledge of connectivity, it can only draw
bonds through distance calculatoin between consecutively numbered atoms.
Perhaps there is a misnumbering of the .gro file.

On 2012-09-24 07:48:17AM -0700, Shima Arasteh wrote:
> 
> 
>  In fact, the structure visualized by VMD and choosing line as draw style is 
> ok, but the second structure of protein ( I mean the choosing ribbons) shows 
> a broken structure. How come? what does it mean?
> 
> Thanks in advance.
> 
> 
> Sincerely,
> Shima
> 
> 
> - Original Message -
> From: Justin Lemkul 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Cc: 
> Sent: Monday, September 24, 2012 2:09 PM
> Subject: Re: [gmx-users] packing lipids
> 
> 
> 
> On 9/24/12 6:22 AM, Shima Arasteh wrote:
> >
> > Dear gmx users,
> >
> > Is it  possible that the protein got broken during shrinking iteration of 
> > packing lipids around the  protein?
> >
> 
> Only if it were broken to begin with.  This is a rather vague statement; if 
> you 
> need further help, you will have to be a lot more specific about what's going 
> on.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> 
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Re: [gmx-users] InflateGro methodology

[Peter C. Lai]

Why don't you just try it and see what happens?

On 2012-09-23 12:19:20AM -0700, Shima Arasteh wrote:
> 
> 
> Dear users,
> 
> I wanna pack the lipids around my protein. To do so, InflateGro methodology 
> is applied. Following Justin's tutorial KALP15-DPPC, the first step is 
> scaling up 4 times:
> # perl inflategro.pl system.gro 4 POPC 14 system-inflated.gro 5 area.dat
> and then shrinking it for 26 times. 
> 
> I'd like to know if it is possible to scale up 6 times or more and then scale 
> it down for around 30 times? Because when I scale up 4 times, I see 2,3 lipid 
> chains are still in contact with the protein (I am not sure if this would be 
> a major problem or not!) . 
> 
> 
> Would you please advise me?
> 
> Thanks in advance. 
> 
> Sincerely,
> Shima
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Re: [gmx-users] Domain decomposition error, is mdrun_mpi now obsolete?

[Peter C. Lai]

There are 2 ways to build a parallel gromacs. For shared memory clusters you
still need to use MPI, but if all your cores are on one host, you can build
it without MPI which will make an mdrun that uses threading.

Domain Decomposition is tied in with the size of the simulation and PME, so 
it's not anything to do with MPI. If your simulation is too small, there 
isn't enough volume to slice into domains larger than the minimum cell size
(you need at least 1 chargegroup/particle and its group of neighbors per 
domain). Since you started off by using MPI, you told mpirun and mdrun to
use 6 CPUs so it tried to, then couldn't, so it gave you an error :)
(although this happens with the threaded version too - mdrun defaults to the
highest number of processors specified by the command, then determines the DD
matrix, then tries to chunk out the simulation to fit that matrix).

On 2012-09-22 03:05:23PM -0700, Ladasky wrote:
> Hello again everyone,
> 
> I'm currently running GROMACS 4.5.4 on Ubuntu Linux 11.10.  I'm trying to
> clean up my simulation conditions.  Many of my MDP files are hold-overs from
> earlier versions of GROMACS, as far back as v. 3.3.  I have written some
> shell scripts which should handle this work automatically -- that is, as
> long as I get no errors.
> 
> I have a six-core CPU, and my scripts invoke mdrun_mpi to take advantage of
> the parallel processors.
> 
> While doing my cleanup work, I just got my first domain decomposition error
> message:
> 
> http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm
> 
> Of course, I'll need to work on fixing that error -- though why GROMACS
> would complain about having too many CPUs at its disposal, rather than just
> running with fewer CPUs, is a bit of a mystery to me.
> 
> Reading through the comments at that link, I surmise that I may no longer
> need to download and build a separate MPI package, that multiprocessing is
> the default behavior of mdrun.  Is that correct?
> 
> 
> 
> 
> --
> View this message in context: 
> http://gromacs.5086.n6.nabble.com/Domain-decomposition-error-is-mdrun-mpi-now-obsolete-tp5001240.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Strong position restrain

[Peter C. Lai]

Postion restraints for a given topology must appear in the same section as
the current molecule's toplogy before the next new [molecule_type].

So you need to #include position_restraints.itp after the topol.itp.:

 #include "topol_Protein_A.itp"
 #ifdef POSRE
 #include "strong_posre.itp"
 #endif
 #include "topol_Protein_B.itp"
 #ifdef POSRE
 #include "strong_posre.itp"
 #endif

On 2012-09-22 02:39:58AM -0700, Shima Arasteh wrote:
> Dears,
> 
> As explained it many times before, I am simulating a system of water, dimer 
> protein and water. I am doing this simulation by getting idea from 
> KALP15-DPPC tutorial. 
> 
> First of all, when I get the top file, I don't see the section of position 
> restrains in top file. My generated top file is as below:
> 
> ; Include forcefield parameters
> #include "./charmm36-modified.ff/forcefield.itp"
> 
> ; Include chain topologies
> #include "topol_Protein_A.itp"
> #include "topol_Protein_B.itp"
> 
> ; Include POPC chain topology
> #include "popc.itp"
> 
> ; Include water topology
> #include "./charmm36-modified.ff/tip3p.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcx    fcy    fcz
>    1    1   1000   1000   1000
> #endif
> 
> ; Include topology for ions
> #include "./charmm36-modified.ff/ions.itp"
> 
> [ system ]
> ; Name
> Gromacs Runs One Microsecond At Cannonball Speeds
> 
> [ molecules ]
> ; Compound    #mols
> Protein_A    1
> Protein_B    1
> 
> 1. I'd like to know why? Is it not expected?
> 
> Secondly, to put a strong position restrain on protein, I added the "Strong 
> position restraints for InflateGRO" after FF section. grompp gives me an 
> error of invalid order:
> Fatal error:
> Syntax error - File strong_posre.itp, line 3
> Last line read:
> '[ position_restraints ]'
> Invalid order for directive position_restraints
> 
> 
> 2. Would you please give me your suggestion? 
> 
> Thanks in advance.
> 
>  
> Sincerely,
> Shima
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Genetics, Div. of Research  | 705 South 20th Street
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Re: [gmx-users] About Bond in Topology

[Peter C. Lai]

Also, if you have specified the bond in .top file properly then gromacs
should consider a bond there. Run some MD to see if the bond stays intact...

On 2012-09-22 02:23:13PM +0800, vidhya sankar wrote:
> Thank you Sir. For your repl
> 
> 
> I Would like to construct .top file for Cyclic Peptide .
> My N-terminal residue is ARG  and C-Terminal is  
> PRO .  In pdb There is Bond between N atom of ARG (First residue)  and C 
> atom  of  PRO (Last Residue) When I Generated Topology using pdb2gmx .  But  
> there is No bond connectivity Between First and Last Atom .Then 
> Manually I have  Edited  .top file and I have defined  the bond Between 
> First Atom  (1) and Last atom (169) . Then I have done EM Successfully .
> My Question Is 
> 
> Will  This  Manual Editing of .top File  create a bond or Not . 
> 
> With Regards
> S.Vidhyasankar
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Genetics, Div. of Research  | 705 South 20th Street
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(205) 690-0808  |
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Re: [gmx-users] About Bond in Topology

[Peter C. Lai]

You should probably consult the previous emails that Mark has already sent
on the subject.

On 2012-09-22 02:23:13PM +0800, vidhya sankar wrote:
> Thank you Sir. For your repl
> 
> 
> I Would like to construct .top file for Cyclic Peptide .
> My N-terminal residue is ARG  and C-Terminal is  
> PRO .  In pdb There is Bond between N atom of ARG (First residue)  and C 
> atom  of  PRO (Last Residue) When I Generated Topology using pdb2gmx .  But  
> there is No bond connectivity Between First and Last Atom .Then 
> Manually I have  Edited  .top file and I have defined  the bond Between 
> First Atom  (1) and Last atom (169) . Then I have done EM Successfully .
> My Question Is 
> 
> Will  This  Manual Editing of .top File  create a bond or Not . 
> 
> With Regards
> S.Vidhyasankar
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
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(205) 690-0808  |
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Re: [gmx-users] Visualizing the system

[Peter C. Lai]

This is a VMD question, but try using manual selections, like:

"not resname POPC and not resname SOL and not resname NA and not resname CL" 
as a selection that doesn't show popc, water, and ions, for example.

I haven't had issues with VMD confusing what a protein is or not, so maybe
there is a residue ordering issue or something going on with the gro file?

On 2012-09-21 11:19:51PM -0700, Shima Arasteh wrote:
> 
> 
> Hi,
> In order to see a system of protein and lipids, I use VMD. I called 
> system.gro something similar to what is produced in KALP15 in DPPC. When I 
> load system.gro and select protein, one of lipids is loaded with it. 
> I am wondering if it is a problem with my system.gro? Or something with the 
> applied visualization tool? 
> 
> Thanks in advance.
> 
> Sincerely,
> Shima
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] About Presence of Bond In Topology

[Peter C. Lai]

Molecular visualization programs determine bonds through distance
measurements. Especially since .gro files do not contain connectivity
information. The topology is where the bond infomration is stored.
So check there...

On 2012-09-22 12:33:31PM +0800, vidhya sankar wrote:
> 
> 
> Dear Justin Thank you for your Reply
> 
> After pdb2gmx When i Visualize the resultant .gro file  of  my cyclic peptide 
> in VMD 
> 
> I have Observed the Bond Between  Nitrogen atom (N ) of First residue and 
> Carbon atom (C) of Last residue   I have not observed The same bond when I 
> open and Visualize in Chimera .  Then How Could i Confirm Whether the bond is 
> present or Not?
> 
> Thanks in Advance
> 
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======
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] TIP4P water model

[Peter C. Lai]

Perhaps genion is not removing the dummy atoms properly?

On 2012-09-21 04:48:37PM +0100, Ankita naithani wrote:
> Hi all,
> 
> I am trying to begin a simulation of a protein.
> 
> I am using AMBER99sb-ILDN force field and TIP4P water model. However,
> I am facing a problem in the ion adding step.
> 
> when  I issue the grompp command to generate the necessary .tpr file
> for simulation to be utilised by genion tool, I get the following
> error :
> 
> "Fatal error:
> number of coordinates in coordinate file (system_solv.gro, 421880)
>  does not match topology (topol.top, 416008)
> "
> 
> However, I have rechecked several times my topology file and the
> co-ordinate file and I am running it pretty straightforward to get
> this error. When I try TIP3P water model for the same protein, I do
> not get the error.
> 
> I get the same error when I use TIP4P-Ew water model too. I have
> decide a better water model for my system before I run my final
> production simulations and so I have been trying to compare both the
> water models. I am wondering if anyone could kindly suggest the
> possible reason for this error because ideally, it should not be
> giving me any error at this stage as I haven't manipulated with
> anything.
> 
> I am also appending my ions.mdp info below:
> 
> ; ions.mdp - used as input into grompp to generate ions.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator= steep ; Algorithm (steep = steepest descent 
> minimization)
> emtol = 1000.0; Stop minimization when the maximum force < 
> 1000.0 kJ/mol/nm
> emstep  = 0.01  ; Energy step size
> nsteps= 5 ; Maximum number of (minimization) 
> steps to perform
> 
> ; Parameters describing how to find the neighbors of each atom and how
> to calculate the interactions
> nstlist   = 1 ; Frequency to update the neighbor list 
> and long range forces
> ns_type   = grid  ; Method to determine neighbor list 
> (simple, grid)
> rlist = 0.9   ; Cut-off for making neighbor list (short range 
> forces)
> coulombtype   = PME   ; Treatment of long range electrostatic 
> interactions
> rcoulomb  = 0.9   ; Short-range electrostatic cut-off
> rvdw  = 0.9   ; Short-range Van der Waals cut-off
> pbc   = xyz   ; Periodic Boundary Conditions (yes/no)
> 
> ---
> 
> 
> 
> -- 
> Ankita Naithani
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Programmer/Analyst  | KAUL 752A
Genetics Div. of Research   | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Water molecule can not be settled - mdrun error

[Peter C. Lai]

On 2012-09-21 02:59:17PM -0400, Justin Lemkul wrote:
> 
> 
> On 9/21/12 1:31 PM, Lara Bunte wrote:
> > Hi Justin
> >
> > I used this settings except of vdw-type = switch and rvdw_switch = 0.8 and 
> > with this settings grompp gives me two notes and one of this notes is 
> > inconsistent:
> >
> > NOTE 1 [file pr.mdp]:
> >For energy conservation with switch/shift potentials, rlist should be 0.1
> >to 0.3 nm larger than rvdw.
> >
> > Because I thought rlist hast to be 1.2 and rvdw hast to be 1.2 for my 
> > CHARMM27 force field.
> >
> >
> 
> Increase rlist as suggested to accommodate the algorithm.  Since CHARMM does 
> not 
> use charge groups (well, it uses single-atom charge groups) this isn't such a 
> big deal.  For a force field like Gromos96, it matters a lot more.

Actually rlist has to be equal to rvdw for this case (PME will complain if it
doesn't). I haven't had a water settling issue in a correctly setup system
with rlist = rvdw and a switched rvdw.  I do remember a bug in the code that
forgets rlistlong is specified.

> 
> >
> > My second note is:
> >
> > NOTE 2 [file pr.mdp]:
> >The sum of the two largest charge group radii (0.079505) is larger than
> >rlist (1.20) - rvdw (1.20)
> >
> >
> > which I sadly don't understand.
> >
> 
> http://www.gromacs.org/Documentation/Errors?highlight=errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
> 
> -Justin
> 

I also get this note too, but the sum looks fine to me. If the sum > 0.15 then
it typically indicates chargegroups are being used, which they shouldn't for 
charmm-based forcefields, but in this case the distance shown is on the order
of a heavy-h bond. I think the note message is still related to rlist vs. 
rlistlong.

anyway, I routinely ignore both these notes and it hasn't given me problems
so far. I would still go bck to check the specific water that could not settle
and see what the other particles near it are since that is probably the root
of the problem. Also, we haven't been told what the results of the energy 
minimzation was...

-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
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(205) 690-0808  |
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Re: [gmx-users] Re: v-rescale

[Peter C. Lai]

On 2012-09-20 12:18:02AM -0700, Ladasky wrote:
> Hi Peter,
> 
> Thanks for your response.
> 
> Rather than dragging this thread too far off-topic, I'll direct you back to
> my thread, where I have just posted additional details.  I took a warning
> message from GROMACS a bit too literally and it caused me to use conditions
> that blew up my simulations.
> 
> I am interested in your protocol for "the typical equilibration."  If this
> is in fact standardized, do you have a reference?  It doesn't match up with
> anything in the tutorial files I have been using to run my own simulations. 
> Admittedly, those files are from GROMACS 3.3, and the procedures may be a
> bit out of date.
> 

Generally it's probably not a good idea to rely on tutorials designed 
around 3.3 when a google search for gromacs tutorial shows a series of 4.5.x 
tutorials written by Justin himself, with explanations of why certain steps
are conducted. (also when certain features may be implemented differently,
such as the introduction of the v-rescale thermostat).

-- 
==========
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Re: v-rescale

[Peter C. Lai]

I am not sure where the idea of using berendsen barostat with the v-rescale 
thermostat for equilibration came from, however. Doesn't the typical 
equilibration begin with v-rescale for temperature equilibration then 
adding parinello-rahman barostat then switching to nose-hoover for production 
runs (as nose-hoover chains result in the correct canonical distribution)?

On 2012-09-19 04:24:27PM -0700, Ladasky wrote:
> Dear Sara,
> 
> I just had a problem with my simulations that I traced to the use of the
> V-rescale temperature algorithm.  Here is my recent post:
> 
> http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-td4999302.html;cid=1348087067061-71#a5001121
> 
> V-rescale may be appropriate in certain simulations, but it is apparently
> NOT appropriate when used with Berendsen pressure coupling during the
> initial equilibration.  I don't know if that is related to your problem, but
> it's something that I just discovered the hard way.
> 
> 
> 
> --
> View this message in context: 
> http://gromacs.5086.n6.nabble.com/v-rescale-tp5001066p5001122.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> -- 
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==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Energy Minimization of Alanin

[Peter C. Lai]

for EM you can probably ignore this, but note that these are the wrong
cutoffs for CHARMM27. (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2 
rvdw_switch=0.8 and vdwtype=switch).

On 2012-09-19 11:04:47AM +0100, Lara Bunte wrote:
> Hello
> 
> I want to do md simulations with the amino acid alanin for practice. I choose 
> alanin because it is parametrized in my forcefield. I use charmm27.
> 
> I created with pdb2gmx my topology and I use water model tip3p. I choosed a 
> dodecahedron box with distance of 0.5 between the solute and this box. With 
> genbox and the solvation I used spc216 model. 
> 
> Next I want to run an energy minimization and I create this em.mdp file:
> 
> integrator     = steep 
> emtol      = 1000.0  
> emstep       = 0.01  
> nsteps    = 5000  
> 
> nstlist = 1   
> rlist    = 0.7  
> coulombtype   = PME    
> rcoulomb    = 0.7 
> vdw-type    = cut-off    
> rvdw  = 0.7   
> nstenergy  = 10
> 
> grompp works but I got this note:
> 
> 
> NOTE 1 [file em.mdp]:
>   The optimal PME mesh load for parallel simulations is below 0.5
>   and for highly parallel simulations between 0.25 and 0.33,
>   for higher performance, increase the cut-off and the PME grid spacing
> 
> Is this necessary for me to increase cut-off and PME grid spacing or can I 
> ignore this note? I would be thankful if you could explain that to me. 
> 
> 
> Thanks for help
> 
> Greetings
> Lara
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Extracting bond information from topol.tpr file using template.c

[Peter C. Lai]

I forgot to mention that the bond info should be in the .tpr file somewhere
as it was processed from the topology and I think gmxdump will also show
the connectivities.

On 2012-09-18 10:49:25PM -0400, Amit Shavit wrote:
> Hello,
> 
> I'm relatively new to GROMACS, and I need to write some of my own analysis
> tools using the template.c file.
> I have been able to figure out most of the structure of it, and how the C
> Structs are used. That is to say, I can successfully retrieve particle
> positions, residue IDs, residue names, etc.
> 
> The one piece of information that I can't seem to be able to retrieve is
> bonding information. Is there a way for me to get this? I should mention
> that I run the program by inputting a traj.trr and topol.tpr files, so I
> have access to the information saved in those files.
> 
> Thanks!
> Amit
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] Extracting bond information from topol.tpr file using template.c

[Peter C. Lai]

The topol.top/.itp files have the pairwise bond information.

On 2012-09-18 10:49:25PM -0400, Amit Shavit wrote:
> Hello,
> 
> I'm relatively new to GROMACS, and I need to write some of my own analysis
> tools using the template.c file.
> I have been able to figure out most of the structure of it, and how the C
> Structs are used. That is to say, I can successfully retrieve particle
> positions, residue IDs, residue names, etc.
> 
> The one piece of information that I can't seem to be able to retrieve is
> bonding information. Is there a way for me to get this? I should mention
> that I run the program by inputting a traj.trr and topol.tpr files, so I
> have access to the information saved in those files.
> 
> Thanks!
> Amit
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==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] LINCS warning in md run

[Peter C. Lai]

Looks like there is still something clashing with atom 979.
The resulting force after EM was close to 1, which is not very much
minimized at all...

What is atom 979 and what is near it?

On 2012-09-18 01:22:25PM +0200, reising...@rostlab.informatik.tu-muenchen.de 
wrote:
> I need the rest of the structure just as it is now because I want to do
> electrostatic analysis with it.
> I just added the phosphate manually and so I want to minimize and run a
> short MD with it.
> 
> I added the dihedraltype of the amber database
> (http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p)
> to the ffbonded file.
> And additionally I looked at the protein and made all the residues which
> could somehow influence the protein flexible so that eventual clashes can
> be repaired.
> But still I got the error:
> 
> ..Step 3612, time 3.612 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.08, max 0.31 (between atoms 975 and 978)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> 976979   32.60.0961   0.0960  0.0960
> 
> Step 3613, time 3.613 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000237, max 0.001400 (between atoms 976 and 979)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> 976979   33.40.0960   0.0959  0.0960
> ..
> 
> Too many LINCS warnings (1000)
> 
> 
> I already minimized the protein and everything was fine. There were no
> errors:
> 
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -7.7436938e+05
> Maximum force =  8.6871973e+03 on atom 979
> Norm of force =  7.1224258e+01
> 
> gcq#49: "You Could Make More Money As a Butcher" (F. Zappa)
> 
> 
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -7.7436938e+05
> Maximum force =  8.6871973e+03 on atom 979
> Norm of force =  7.1224258e+01
> 
> 
> And also during the grompp run there are no errors.
> Can you please help me to find out where the problem lies?
> 
> 
> Thank you,
>  Eva
> 
> 
> >
> >
> > On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
> >> Ah okey. Thank you.
> >> I will write them.
> >>
> >> Hmm, but the protein is a crystal structure from pdb with a resolution
> >> of
> >> 1.2. I already added the hydrogen atoms to this structure and there I
> >> already minimized them and made a md run. And there were no errors. And
> >> now I only added the phosphate to the minimized structure. So I thought
> >> that I only had to minimize the phosphate and the residue it bound on.
> >> Or is there a mistake in my thought here?
> >
> > If adding the phosphate resulted in a crash, then clearly that's the
> > problem.  I
> > don't understand why you would run EM on just the phosphate and keep the
> > rest of
> > the protein structure frozen.  Again, that potentially prevents clashes
> > from
> > being resolved.  I don't understand what value there is in only minimizing
> > the
> > phosphate.
> >
> > -Justin
> >
> > --
> > 
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> > --
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> >
> 
> 
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Re: [gmx-users] make index groups with make_ndx

[Peter C. Lai]

The selections are boolean (like a search).

So to include both 6 and 7 you would use 6 | 7 (make the selection of 6 or 7)

so you probably want something like ! res65 | ! res 6 etc.


On 2012-09-18 10:56:14AM +0200, reising...@rostlab.informatik.tu-muenchen.de 
wrote:
> Hi everybody,
>  I want to make two index groups for my protein. The first one should
> contain the whole protein except of the residues :
> TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80
> 
> I tried it with the arguments:
> "protein" &! res 65 &! res 6 &! res 7 &! res 61 &! res 64 &! res 80
> "protein" &! res 65 6 7 61 64 80
> 
> Both didn't work.
> 
> The other index group should only contain the residues:
> TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80
> 
> Here I tried:
> res 6 & res 7 & res 61 & res 64 & res 65 & res 66
> 
> This worked.
> 
> So I don't understand why the negation of this command did not work in the
> first index group.
> 
> Can you please help me?
> 
> Thank you,
>  Eva
> 
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==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] Charmm for Proteins

[Peter C. Lai]

charmm27 is the canonical charmm protein FF, which is supported by gromacs.
Note that if you are using gromacs prior to 4.5.5 to use -nochargegrp when
using pdb2gmx when parameterizing your protein.

On 2012-09-13 04:19:16PM +0100, Steven Neumann wrote:
> Dear All,
> 
> Could you please write me which is the latest version of Charmm force
> field for proteins? I want to study protein folding in explicit
> solvent. Is it available in Gromacs?
> 
> Steven
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-- 
==========
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] MD problem with nwall=2

[Peter C. Lai]

On 2012-09-06 02:46:21PM +0200, Bogdan Costescu wrote:
> On Wed, Sep 5, 2012 at 8:37 PM, Peter C. Lai  wrote:
> > Could be a result of not setting x/y compressibility = 0 as the manual
> > suggests you should do...
> 
> As one who has also tried to use walls recently, I've also found this
> statement in the manual, but no further explanation. Anyone cares to
> expand on it ?
> 
> For testing, I've recently performed a run with compressibility=0 for
> z and non-zero for x/y (so, exactly opposite to what the manual
> suggests :)). The box deformed as expected in x/y and the pressure
> seemed to be maintained correctly. Is there some reason for which this
> would be a random (i.e. not easily reproducible) result ? Or are there
> some less obvious problems with it ?

I am trying to use walls with lipid bilayers. I once also applied a non-zero
compressibility to x/y , and my bilayer physically collapsed in less than 1ns,
although the simulation appeared to be otherwise nominal.

Another thing I noticed was that the value of wall_density is important, 
since a small leakage past the wall may not be noticeable until you exceed 
1-10ns and that will quickly drop volume to 0 and make it look like x/y has 
collapsed (and cause a system crash due to exceeding pme/dd tolerances).

-- 
==========
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics Div. of Research   | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] MD problem with nwall=2

[Peter C. Lai]

Could be a result of not setting x/y compressibility = 0 as the manual
suggests you should do...

On 2012-09-05 11:28:30AM +, 김현식 wrote:
> 
> Dear Experts
> Hello. 
> I have tried to run md simulation with wall option, which included "nwall=2". 
> However, there have been some problems. Always, the running is down with no 
> error message or a message like below.
> ---Program mdrun_mpi_d, 
> VERSION 4.5.3Source code file: ns.c, line: 2544
> Fatal error:One of the box vectors has become shorter than twice the cut-off 
> length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.For 
> more information and tips for troubleshooting, please check the 
> GROMACSwebsite at 
> http://www.gromacs.org/Documentation/Errors---
> And at this point, my triclinic system was getting larger in both 
> Z-directions, and was getting smaller in X and Y directions.In my thinking, 
> it may be happen because of changing the box. Can anyone who have experience 
> like that or how to handle this give me some advise?
> I attach some parts of my mdp file to run md.  ; Temperature coupling is on 
> tcoupl  = V-rescale ; modified Berendsen thermostat tc-grps   
>   = Protein Non-Protein   ; two coupling groups - more accurate tau_t 
>   = 0.1   0.1 ; time constant, in ps ref_t   = 300   300 ; 
> reference temperature, one for each group, in K   ; Pressure coupling is on 
> pcoupl  = Berendsen ; Pressure coupling on in NPT pcoupltype  
> = semiisotropic ; uniform scaling of box vectors tau_p   = 2.0 
> 2.0  ; time constant, in ps ref_p   = 1.0 1.0  ; 
> reference pressure, in bar compressibility = 4.5e-5 4.5e-5   ; isothermal 
> compressibility of water, bar^-1   ; Periodic boundary conditions pbc 
> = xy   ; 2-D PBC   
>  ;Wall nwall   = 2 ;  wall_type= 9-3wall_r_linpot 
>= 1   wall_atomtype   =  opls_001 opls_001wall_density= 20 20   
> wall_ewald_zfac= 3 ewald_geometry  = 3dc   ;
> 
> 
> 
> Thank youHyunsik
> -- 
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Re: [gmx-users] Is there a way to redirect utility output to the screen, rather than to a file?

[Peter C. Lai]

Have you tried to write to a named pipe? Like mkfifo coord.xvg then 
g_traj -ox coord.xvg? Then tail -F coord.xvg?

I'm not sure this is less work than just letting it write the xvg and then
looking at the xvg (and deleting it later)...

On 2012-09-03 08:26:56PM -0400, Andrew DeYoung wrote:
> Hi,
> 
> Sometimes, I want to take a quick look at a certain property using one of
> the Gromacs utilities.  For example, I might want to use:
> 
> g_traj -f traj.trr -s topol.tpr -n index.ndx -nox -noy -b 5 -e 10 -ox
> coord.xvg
> 
> to look at the z-component of the group specified in index.ndx from t = 5 ps
> to 10 ps.  I can save this data in an .xvg file (coord.xvg) using the -ox
> switch.  
> 
> However, what if I would rather not save the data to an .xvg file (since I
> just want to take a quick look)?  Does anyone know if it is possible to
> redirect the output of g_traj to the screen, rather than to coord.xvg?
> 
> Thank you so much for your time! 
> 
> Andrew DeYoung
> Carnegie Mellon University
> 
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Re: [gmx-users] Adding phosphate to protein

[Peter C. Lai]

You'll have to do it manually. Perhaps VMD or Chimera can help you with 
adding the atoms to the initial pdb.
Then you'll have to create a modified amino acid topology for the amino acid
that is getting phosphorylated in your forcefield's .rtp file.

On 2012-09-03 10:05:08AM +0200, reising...@rostlab.informatik.tu-muenchen.de 
wrote:
> I want to add the phosphor first.
> And I hoped that there is a program just like the "pdb2gmx" which adds
> hydrogens to the protein.
> 
> > You haven't anwsered my question. Did you just want to add the phosphate
> > before starting the simulation or were you hoping for the simulation to do
> > it
> > for you?
> >
> >
> > On 2012-09-03 09:51:12AM +0200,
> > reising...@rostlab.informatik.tu-muenchen.de wrote:
> >> Hi,
> >> I have my protein without phosphorylations and now I want to
> >> phosphorylate
> >> one residue of my protein.
> >> Is this possible?
> >>
> >> Thank you
> >>
> >> > can you be a bit more specific? Are you expecting to phosphorylate the
> >> > protein along the trajectory or did you want to run continuous
> >> simulations
> >> > with different phosphorylation states?
> >> >
> >> >
> >> > On 2012-09-03 09:30:58AM +0200,
> >> > reising...@rostlab.informatik.tu-muenchen.de wrote:
> >> >> Hi everybody,
> >> >>
> >> >> I want to add a phosphate to my protein. Is this possible with
> >> gromacs?
> >> >>
> >> >> Thank you
> >> >>
> >> >> --
> >> >> gmx-users mailing listgmx-users@gromacs.org
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> >> > ==
> >> > Peter C. Lai | University of Alabama-Birmingham
> >> > Programmer/Analyst   | KAUL 752A
> >> > Genetics, Div. of Research   | 705 South 20th Street
> >> > p...@uab.edu | Birmingham AL 35294-4461
> >> > (205) 690-0808   |
> >> > ==
> >> >
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> > Programmer/Analyst  | KAUL 752A
> > Genetics, Div. of Research  | 705 South 20th Street
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Re: [gmx-users] Adding phosphate to protein

[Peter C. Lai]

You haven't anwsered my question. Did you just want to add the phosphate 
before starting the simulation or were you hoping for the simulation to do it
for you?


On 2012-09-03 09:51:12AM +0200, reising...@rostlab.informatik.tu-muenchen.de 
wrote:
> Hi,
> I have my protein without phosphorylations and now I want to phosphorylate
> one residue of my protein.
> Is this possible?
> 
> Thank you
> 
> > can you be a bit more specific? Are you expecting to phosphorylate the
> > protein along the trajectory or did you want to run continuous simulations
> > with different phosphorylation states?
> >
> >
> > On 2012-09-03 09:30:58AM +0200,
> > reising...@rostlab.informatik.tu-muenchen.de wrote:
> >> Hi everybody,
> >>
> >> I want to add a phosphate to my protein. Is this possible with gromacs?
> >>
> >> Thank you
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
> > --
> > ==
> > Peter C. Lai| University of Alabama-Birmingham
> > Programmer/Analyst  | KAUL 752A
> > Genetics, Div. of Research  | 705 South 20th Street
> > p...@uab.edu| Birmingham AL 35294-4461
> > (205) 690-0808  |
> > ==
> >
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> 
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Re: [gmx-users] Adding phosphate to protein

[Peter C. Lai]

can you be a bit more specific? Are you expecting to phosphorylate the 
protein along the trajectory or did you want to run continuous simulations 
with different phosphorylation states?


On 2012-09-03 09:30:58AM +0200, reising...@rostlab.informatik.tu-muenchen.de 
wrote:
> Hi everybody,
> 
> I want to add a phosphate to my protein. Is this possible with gromacs?
> 
> Thank you
> 
> -- 
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Re: [gmx-users] Hydrogen bond breaking process

[Peter C. Lai]

Well there is always ReaxFF. You'd still have to use QM/MM to parameterize 
the various states though.

On 2012-09-02 09:48:25PM -0400, Justin Lemkul wrote:
> 
> 
> On 9/2/12 9:42 PM, Rajiv Gandhi wrote:
> > Could you tell me how can i perform for coordinate covalent bond breaking
> > and forming between Fe-CO in myoglobin. I guess, it has been already done
> > by some groups. If possible can you send me journals related to this.
> 
> You can't break and form bonds in classical MD.  That's an exercise for 
> QM/MM. 
> There are plenty of articles out there, a Google search would turn up 
> hundreds, 
> maybe even some directly related to what you want to do.
> 
> -Justin
> 
> > Thanks.
> >
> > On Mon, Sep 3, 2012 at 8:55 AM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 8/31/12 10:43 PM, Rajiv Gandhi wrote:
> >>
> >>> Can you tell me "how to predict the Hydrogen bond breaking process (For
> >>> example Fe-CO hydrogen bond broken in Myoglobin at 100 ps) through MD
> >>> simulation?
> >>>
> >>>
> >> There is no hydrogen bonding in a Fe-CO interaction.  That is a coordinate
> >> covalent bond.  If you want to study hydrogen bonds breaking and forming in
> >> protein structures, the pull code may be useful.
> >>
> >> -Justin
> >>
> >> --
> >> ==**==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Research Scientist
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>
> >> ==**==
> >> --
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> >
> >
> >
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
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Genetics, Div. of Research  | 705 South 20th Street
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(205) 690-0808  |
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Re: [gmx-users] what's the difference between gen_seed and ld_seed?

[Peter C. Lai]

On 2012-08-23 08:06:12PM +0200, Albert wrote:
> hello :
> 
>I am a little bit confused about the difference between gen_seed and 
> ld_seed. I checked the manual, it is said:
> 
> gen_seed
> used to initialize random generator for random velocities, when gen_seed 
> is set to -1, the seed is calculated from the process ID number.
> This is often used coupled with gen_vel which is Generate velocities in 
> grompp according to a Maxwell distribution at temperaturegen_temp [K], 
> with random seed gen_seed. This is only meaningful with integratormd.
> 
> As indicated in Jonhn E.Kerrigan's tutorial, gen_seed=-1 is always 
> turned on in NVT, NPT and MD production step. However, in Justin's 
> Lysozyme in Water tutorial, this option is only turned on in NVT and the 
> following NPT and MD production were turned off.

Yes because you undo your equilibration when you reassign initial
velocities using gen_seed in NPT and MD production (NPT) (md/md-vv 
integrator).

> 
> I am just wondering which option would be better for our simulations?
> 
> How about ld_seed? here is the statement from manual:
> 
> ld_seed: (1993) [integer]
> used to initialize random generator for thermal noise for stochastic and 
> Brownian dynamics. When ld_seed is set to -1, the seed is calculated 
> from the process ID. When running BD or SD on multiple processors, each 
> processor uses a seed equal to ld_seed plus the processor number.
> 
> when should we turn this option on?

As stated, you use this option for use with the bd or sd integrators.

-- 
==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] very strange area/lipid value for POPC membrane system

[Peter C. Lai]

Also important to ask is:
What was your APL *before* you inserted the protein? Was it realistic to 
begin with? If not, then start your problem solving there...

On 2012-08-19 06:16:48PM +0200, Albert wrote:
> Dear All:
> 
>   I am using GridMAT-MD to calculate the area/lipid for my POPC system. 
> The whole system was consist of a 300aa protein, 116 POPC and 0.15M NaCl.
> 
> 
> 1. I calculate the area/lipids by GridMAT-MD with the protein in it and 
> I got a value:
> 
> Ave APL = 54.1013569676733 sq. Ang
> 
> 2. I removed the protein and I get another value:
> 
> Ave APL = 76.1121752016697 sq. Ang
> 
> Do you have any idea what happen for my calculation?  Of course I truned 
> the line "proteinyes/no" for case with/without protein in the 
> example param file. What need to mention is that both values are far 
> from the POPC real area/lipids which should be something around 64.
> 
> Does anybody knows what happen?
> 
> thank you very much
> 
> best
> Albert
> 
> 
> here is paramters:
> 
> 
> ## Input file and input file parameters
> 
> bilayereq-withProtein.gro
> solventSOL
> ionsNA+,CL-
> 
> resname  POPC
> atomnameP1,C1
> 
> ## Define the size and shape of the grid
> 
> box_sizevectors
> vectors6.57174,6.89896,9.23361
> grid20
> conserve_ratioyes
> 
> ## Define whether there is a protein embedded in the bilayer
> 
> proteinyes
> precision1.3
> P_value5.0
> 
> ## Define the desired output files
> 
> top_pbcno
> bottom_pbcno
> average_pbcno
> 
> top_areayes
> bottom_areayes
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
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Re: [gmx-users] Protein-POPC bilayer

[Peter C. Lai]

On 2012-08-16 09:04:35PM -0700, Shima Arasteh wrote:
> 
> 
> Oh, It's OK. Thanks Peter. :-)
> I used the the same .mdp file sent me by you 1 month ago, for the 
> pre-equilibration of POPC in water. 
> 

Well if that worked out, then what is the problem?

What do you mean by "pre-equlibration" The only step that happens before
equilibraiton is energy minimzation... If NPT is crashing after EM then
try a few ns of NVT (with a V-rescale thermostat) first, but because VMD
gives you highly ordered bilayer (straight chains), I believe I was able
to go from EM directly to NPT without any problems.

> But as others said here, anisotropic pressure coupling might result in major 
> changes in lipid bilayer. I don't know, but it seems it is better to use 
> anisotropic pressure coupling for the pre-equilibration of bilayer!? Right?! 
> Anisotropic would be a better option? 
> 
> Now, I'd like to know which one is suggested to be used for the 
> pre-equilibration before insertion of protein? Anisotropic is suggested?
> 
> Please make me clear here. Thanks for all explanations.

You are welcome to try using anisotropic pressure coupling. With a system of
the size I put forth, it could be large enough[1] to "buffer" against box 
shearing forces.

[1] Anezo et. al J. Phys. Chem. B 2003, 107, 9424-9433

If you already equilibrated the membrane before insertion then go ahead and 
do the insertion. As was stated before, if the box vectors and area per lipid
are in equilibrium by the end of the equilibration, you should be fine.

> 

> 
> Sincerely,
> Shima
> 
> 
> - Original Message -
> From: Peter C. Lai 
> To: Shima Arasteh 
> Cc: Discussion list for GROMACS users 
> Sent: Friday, August 17, 2012 8:19 AM
> Subject: Re: [gmx-users] Protein-POPC bilayer
> 
> Can't remember why I said that, since it's not what I used. Stupid 
> autocorrect? Sorry!
> 
> On 2012-08-16 08:35:23PM -0700, Shima Arasteh wrote:
> > In  "2.1.6. Membrane bilayer construction" part of the article you 
> > mentioned:
> > 
> > Asingle POPC molecule is parameterized using a
> > CHARMM36 force field conversion for GROMACS7. The result-
> > ing system,which consists of around 238 lipids is then equilibrated
> > for at least 50 ns at 310 K and 1 atm under NPT ensemble with
> > anisotropic pressure coupling or until the are a per lipid converges
> > close to the consensus value of around 63–65Å per headgroup.
> > 
> > This is where I asked the question about.
> > 
> > Thanks.
> > 
> >  
> > 
> >  
> > Sincerely,
> > Shima
> > 
> > 
> > - Original Message -
> > From: Peter C. Lai 
> > To: Shima Arasteh ; Discussion list for 
> > GROMACS users 
> > Cc: 
> > Sent: Friday, August 17, 2012 7:17 AM
> > Subject: Re: [gmx-users] Protein-POPC bilayer
> > 
> > Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, 
> > in caes you lost it from the time before:
> > You can choose to use V-rescale and Berendsen if you want but the 
> > Nose-Hoover/
> > Parinello-Rahman with the paraeters below was stable for me with 238 POPC
> > and 21524 water.
> > 
> > 
> > integrator      = md            ; leap-frog integrator
> > nsteps          = 250         ; 2 * 5 = 100 ps
> > dt              = 0.002         ; 2 fs
> > ; Output control
> > nstxout         = 1000           ; save coordinates every 0.2 ps
> > nstvout         = 1000           ; save velocities every 0.2 ps
> > nstenergy       = 100           ; save energies every 0.2 ps
> > nstlog          = 100           ; update log file every 0.2 ps
> > 
> > continuation    = yes            ; NOT first dynamics run
> > constraint_algorithm = lincs    ; holonomic constraints
> > constraints     = h-bonds     ; all bonds (even heavy atom-H bonds) 
> > constrained
> > lincs_iter      = 1             ; accuracy of LINCS
> > lincs_order     = 4             ; also related to accuracy
> > ; Neighborsearching
> > ns_type         = grid          ; search neighboring grid cells
> > nstlist         = 5             ; 10 fs
> > rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
> > rlistlong       = 1.4
> > rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
> > rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
> > vdwtype         = switch
> > rvdw_switch     = 0.8
> > ; Electrostatics
> > coulombtype     = PME           ; Particle Mesh Ewald for long-range 
> > electrostatics
> > pme_order      

Re: [gmx-users] Protein-POPC bilayer

[Peter C. Lai]

Can't remember why I said that, since it's not what I used. Stupid 
autocorrect? Sorry!

On 2012-08-16 08:35:23PM -0700, Shima Arasteh wrote:
> In  "2.1.6. Membrane bilayer construction" part of the article you mentioned:
> 
> Asingle POPC molecule is parameterized using a
> CHARMM36 force field conversion for GROMACS7. The result-
> ing system,which consists of around 238 lipids is then equilibrated
> for at least 50 ns at 310 K and 1 atm under NPT ensemble with
> anisotropic pressure coupling or until the are a per lipid converges
> close to the consensus value of around 63–65Å per headgroup.
> 
> This is where I asked the question about.
> 
> Thanks.
> 
>  
> 
>  
> Sincerely,
> Shima
> 
> 
> - Original Message -
> From: Peter C. Lai 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Cc: 
> Sent: Friday, August 17, 2012 7:17 AM
> Subject: Re: [gmx-users] Protein-POPC bilayer
> 
> Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, 
> in caes you lost it from the time before:
> You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/
> Parinello-Rahman with the paraeters below was stable for me with 238 POPC
> and 21524 water.
> 
> 
> integrator      = md            ; leap-frog integrator
> nsteps          = 250         ; 2 * 5 = 100 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 1000           ; save coordinates every 0.2 ps
> nstvout         = 1000           ; save velocities every 0.2 ps
> nstenergy       = 100           ; save energies every 0.2 ps
> nstlog          = 100           ; update log file every 0.2 ps
> 
> continuation    = yes            ; NOT first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = h-bonds     ; all bonds (even heavy atom-H bonds) 
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5             ; 10 fs
> rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
> rlistlong       = 1.4
> rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
> vdwtype         = switch
> rvdw_switch     = 0.8
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range 
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = Nose-Hoover     ; modified Berendsen thermostat
> tc-grps         = POPC SOL      ; two coupling groups - more accurate
> tau_t           = 0.5   0.5     ; time constant, in ps
> ref_t           = 300   300     ; reference temperature, one for each group, 
> in K
> pcoupl          = Parrinello-Rahman            ; no pressure coupling in NVT
> pcoupltype      = semiisotropic
> tau_p           = 4
> ref_p           = 1.01325 1.01325
> compressibility = 4.5e-5 4.5e-5
> 
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = no    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = no           ; assign velocities from Maxwell distribution
> ;gen_temp        = 300           ; temperature for Maxwell distribution
> ;gen_seed        = -1            ; generate a random seed
> nstcomm         = 1
> comm_mode       = Linear
> comm_grps       = POPC SOL
> 
> On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote:
> > You always use semi-isotropic for bilayer work. The Z is decoupled from x-y 
> > due to symmetry.
> > 
> > I don't think I mention anything differently in the paper.
> > 
> > Pcoupltype               = semiisotropic
> > 
> > 
> > On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote:
> > > 
> > >  Hi,
> > > 
> > > I have a question about the Protein-POPC system:
> > > To insert a protein in lipid bilayer, I am suggested to simulate POPC in 
> > > water separately before insertion, it might decrease the time of final 
> > > simulation. It's OK!
> > > 
> > > In the article suggested me by dear Peter C. Lai, I read that POPC was 
> > > simulated in anisotropic pressure coupling at first and then after 
> > > insertion of protein, semi-isotropic pressure coupling is applied. 
> > > Now, would you please telling me why you used this pro

Re: [gmx-users] Protein-POPC bilayer

[Peter C. Lai]

Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, 
in caes you lost it from the time before:
You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/
Parinello-Rahman with the paraeters below was stable for me with 238 POPC
and 21524 water.


integrator  = md; leap-frog integrator
nsteps  = 250 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 1000   ; save coordinates every 0.2 ps
nstvout = 1000   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps

continuation= yes; NOT first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rlistlong   = 1.4
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
vdwtype = switch
rvdw_switch = 0.8
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = Nose-Hoover ; modified Berendsen thermostat
tc-grps = POPC SOL  ; two coupling groups - more accurate
tau_t   = 0.5   0.5 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one for each group, in 
K
pcoupl  = Parrinello-Rahman; no pressure coupling in NVT
pcoupltype  = semiisotropic
tau_p   = 4
ref_p   = 1.01325 1.01325
compressibility = 4.5e-5 4.5e-5

; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= no; account for cut-off vdW scheme
; Velocity generation
gen_vel = no   ; assign velocities from Maxwell distribution
;gen_temp= 300   ; temperature for Maxwell distribution
;gen_seed= -1; generate a random seed
nstcomm = 1
comm_mode   = Linear
comm_grps   = POPC SOL

On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote:
> You always use semi-isotropic for bilayer work. The Z is decoupled from x-y 
> due to symmetry.
> 
> I don't think I mention anything differently in the paper.
> 
> Pcoupltype   = semiisotropic
> 
> 
> On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote:
> > 
> >  Hi,
> > 
> > I have a question about the Protein-POPC system:
> > To insert a protein in lipid bilayer, I am suggested to simulate POPC in 
> > water separately before insertion, it might decrease the time of final 
> > simulation. It's OK!
> > 
> > In the article suggested me by dear Peter C. Lai, I read that POPC was 
> > simulated in anisotropic pressure coupling at first and then after 
> > insertion of protein, semi-isotropic pressure coupling is applied. 
> > Now, would you please telling me why you used this procedure?
> > And,
> > Would my system be correct  if I use semi-isotropic pressure coupling 
> > instead of anisotropic pressure coupling for the first step?
> > 
> > Thanks in advance for your replies.
> > 
> > 
> > Sincerely,
> > Shima
> > -- 
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Only plain text messages are allowed!
> > * Please search the archive at 
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> -- 
> ==
> Peter C. Lai  | University of Alabama-Birmingham
> Programmer/Analyst| KAUL 752A
> Genetics, Div. of Research| 705 South 20th Street
> p...@uab.edu  | Birmingham AL 35294-4461
> (205) 690-0808|
> ==
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages a

Re: [gmx-users] Protein-POPC bilayer

[Peter C. Lai]

You always use semi-isotropic for bilayer work. The Z is decoupled from x-y 
due to symmetry.

I don't think I mention anything differently in the paper.

Pcoupltype   = semiisotropic


On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote:
> 
>  Hi,
> 
> I have a question about the Protein-POPC system:
> To insert a protein in lipid bilayer, I am suggested to simulate POPC in 
> water separately before insertion, it might decrease the time of final 
> simulation. It's OK!
> 
> In the article suggested me by dear Peter C. Lai, I read that POPC was 
> simulated in anisotropic pressure coupling at first and then after insertion 
> of protein, semi-isotropic pressure coupling is applied. 
> Now, would you please telling me why you used this procedure?
> And,
> Would my system be correct  if I use semi-isotropic pressure coupling instead 
> of anisotropic pressure coupling for the first step?
> 
> Thanks in advance for your replies.
> 
> 
> Sincerely,
> Shima
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
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-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

[Peter C. Lai]

On 2012-08-15 06:55:59PM +, Christopher Neale wrote:
> Write the authors of the simulation paper that has a "correct" APL for POPE 
> and ask them for an input file.
> That is really the only way to be sure that you are not doing something 
> different than they did.
> In my experience, people are quite willing to provide you with their input 
> file(s).
> If you still get a different APL than they reported, then see if your 
> simulation times are similar and repeat your run
> a few times to see if it's just statistical noise.

The fundamental problem Sebastian will have is that Klauda obtained their
APLs using CHARMM software, and he is trying to reproduce this using 
the forcefield in Gromacs software. So even if the CHARMM input files
were provided, it maybe difficult to exactly reproduce the conditions
in Gromacs (if certain parameters were implemented differently)

> 
> Regarding 323 K, I don't recall... it's just a number that sticks in my head. 
> Perhaps it is for DPPE or DPPC.
> 
> I'd still suggest that you at least try POPC. So your peptide binds more 
> favourably to POPE than to POPC... 
> that alone does not limit you to POPE. Then again, I don;t know exactly what 
> you are trying to do.
> 
> Chris.
> 

It is generally a good idea to use a higher temp than the phase transition
temperature, since during equilibration close to the phase transition 
temp there is a risk of inducing some ordering due to uneven heating.
People run DPPC at 323 because its phase transition temp is 315K. If
POPC's is 271 and people typically run POPC at 300, then it may be wise to 
bump up the running temp of a POPE system. Of course, your APL will 
inflate at higher temperatures...

> 
> -- original message --
> 
> 
> My peptide is known to be more favorably to PE than PC membrane that is why I 
> am using POPE.
> 
> Experimentally, the liquid phase transition is at 298K for POPE (if I am not 
> mistaken). Is your 323K refer to some simulations? 
> 
> At first I wanted to use the new CHARMM36 lipids parameters because they are 
> supposed to solve the previous CHARMM27 issue with the area per lipid. 
> However, I am consistently obtained smaller APL then experiment and I am not 
> able to reproduce the published APL obtained for POPE, even if I am starting 
> from their equilibrated 80-POPE membrane and use same simulation conditions. 
> That was the reason for starting this thread on the mailing list. 
> 
> Unfortunately, my peptide conformational space in solution is only 
> well-represented by CHARMM27 (equivalently in CHARMM36), so I can not use 
> Berger's lipid parameters with OPLS or GROMOS even if it would be preferable 
> as they do not have APL inconsistency and are united-atom.
> 
> I will made some tests in the NPAT ensemble. Perhaps the NPAT effects can be 
> made neglegible by using bigger membrane compared to my peptide's size (?). 
> 
> Sebastien 
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==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

[Peter C. Lai]

hy?
> > > > > >>>>
> > > > > >>>> On 2012-07-23 02:34:31PM -0300, Sebastien Cote wrote:
> > > > > >>>>> There is not much difference when using DispCorr or not. At 
> > > > > >>>>> least on the same time scale as the simulation with switch 
> > > > > >>>>> cutoff from 0.8 to 1.2 nm and on the same time scale.
> > > > > >>>>>
> > > > > >>>>> Should DispCorr be used in all membrane simulations? I thought 
> > > > > >>>>> that we should always use this correction.
> > > > > >>>> I alwasy thought it was actually forcefield dependent. I never 
> > > > > >>>> use it with
> > > > > >>>> CHARMM since the mdp files I used as the basis for mine didn't 
> > > > > >>>> with C27, and
> > > > > >>>> I get acceptable APL with POPC when using the same mdp with C36. 
> > > > > >>>> I haven't
> > > > > >>>> compared the codes for CHARMM to see if dispcorr is builtin to 
> > > > > >>>> the gromacs
> > > > > >>>> implementation or not, but the reason I brought it up is that on 
> > > > > >>>> past
> > > > > >>>> mailing list discussions about TIPS3P, there were reports of 
> > > > > >>>> significant
> > > > > >>>> density differences with and without dispcorr.
> > > > > >>>>
> > > > > >>>>
> > > > > >>>>> Thanks,
> > > > > >>>>>
> > > > > >>>>> Sebastien
> > > > > >>>>>
> > > > > >>>>> 
> > > > > >>>>>> Date: Fri, 20 Jul 2012 12:47:44 -0500
> > > > > >>>>>> From: p...@uab.edu
> > > > > >>>>>> To: gmx-users@gromacs.org
> > > > > >>>>>> Subject: Re: [gmx-users] CHARMM36 - Smaller Area per lipid for 
> > > > > >>>>>> POPE - Why?
> > > > > >>>>>>
> > > > > >>>>>> Did you play with DispCorr?
> > > > > >>>>>>
> > > > > >>>>>> On 2012-07-20 09:46:13AM -0300, Sebastien Cote wrote:
> > > > > >>>>>>> Dear Gromacs users,
> > > > > >>>>>>>
> > > > > >>>>>>> My simulations on a POPE membrane using the CHARMM36 
> > > > > >>>>>>> parameters are giving ''area per lipid'' values well below 
> > > > > >>>>>>> the experimental value (59.75-60.75 Angstroms2). Is their 
> > > > > >>>>>>> someone else experiencing a similar problem? If yes, how did 
> > > > > >>>>>>> you solved it?
> > > > > >>>>>>>
> > > > > >>>>>>> I did the following :
> > > > > >>>>>>>
> > > > > >>>>>>> I used the CHARMM36 parameters kindly provided by Thomas J. 
> > > > > >>>>>>> Piggot on the Users contribution section on Gromacs website.
> > > > > >>>>>>> My starting configuration was taken from : 
> > > > > >>>>>>> http://terpconnect.umd.edu/~jbklauda/research/download.html
> > > > > >>>>>>> It is a POPE membrane of 80 lipids equilibrated in NPT at 
> > > > > >>>>>>> T=310K and P=1atm for 40 ns. It is taken from the article 
> > > > > >>>>>>> Klauda, J. B. et al. 2010 J. Phys. Chem. B, 114, 7830-7843.
> > > > > >>>>>>>
> > > > > >>>>>>> At first, I tested normal TIP3P vs. CHARMM TIP3P and saw that 
> > > > > >>>>>>> normal TIP3P gives smaller Area per lipid of about 2-3 
> > > > > >>>>>>> Angstroms. This was also observed by T.J. Piggot (personnal 
> > > > > >>>>>>> communication) and Tieleman (Sapay, N. et al. 2010 J. Comp. 
> > > > > >>>>&

Re: [gmx-users] desired no of water molecules

[Peter C. Lai]

hmm. What happens if you try -maxsol instead of -nmol? 

On 2012-08-14 10:24:18AM +0530, tarak karmakar wrote:
> This is the ala.gro (alanine dipeptide)  file which does not contain
> any water (SOL) a priori.
> 
> Grunge ROck MAChoS
>22
> 1ACE   HH311   1.267   1.058   1.673
> 1ACECH32   1.364   1.086   1.631
> 1ACE   HH323   1.422   0.996   1.607
> 1ACE   HH334   1.416   1.148   1.705
> 1ACE  C5   1.348   1.183   1.515
> 1ACE  O6   1.381   1.152   1.401
> 2ALA  N7   1.301   1.303   1.549
> 2ALA  H8   1.284   1.324   1.646
> 2ALA CA9   1.290   1.409   1.450
> 2ALA HA   10   1.374   1.399   1.381
> 2ALA CB   11   1.160   1.402   1.371
> 2ALAHB1   12   1.131   1.299   1.351
> 2ALAHB2   13   1.086   1.455   1.431
> 2ALAHB3   14   1.166   1.447   1.272
> 2ALA  C   15   1.301   1.548   1.510
> 2ALA  O   16   1.277   1.567   1.629
> 3NME  N   17   1.337   1.646   1.426
> 3NME  H   18   1.356   1.619   1.330
> 3NMECH3   19   1.344   1.784   1.469
> 3NME   HH31   20   1.408   1.835   1.398
> 3NME   HH32   21   1.250   1.838   1.469
> 3NME   HH33   22   1.394   1.797   1.565
>0.33600   0.84200   0.43300
> 
> 
> If I grep 'SOL' ala_solv.gro , then it is showing
> 
> 4SOL OW   23   0.569   1.275   1.165
> 4SOLHW1   24   0.476   1.268   1.128
> 4SOLHW2   25   0.580   1.364   1.209
> ..
> ...
>   668SOL OW 2015   0.755   0.751   0.211
>   668SOLHW1 2016   0.785   0.679   0.149
>   668SOLHW2 2017   0.716   0.711   0.294
>   669SOL OW 2018   2.632   0.122   2.163
>   669SOLHW1 2019   2.586   0.035   2.180
>   669SOLHW2 2020   2.723   0.119   2.204
>   670SOL OW 2021   0.144   1.914   2.030
>   670SOLHW1 2022   0.179   1.873   1.946
>   670SOLHW2 2023   0.054   1.876   2.050
>   671SOL OW 2024   1.901   2.939   2.162
>   671SOLHW1 2025   2.000   2.928   2.153
>   671SOLHW2 2026   1.861   2.853   2.194
> 
> so certainly it does contain 668 water molecules.
> Thanks,
> 
> On Tue, Aug 14, 2012 at 10:13 AM, Peter C. Lai  wrote:
> > Did you have waters in the system before adding another 612?
> >
> > I don't know how VMD counts waters, but another way is to grep -c for SOL in
> > the resulting gro file and divide by 3.
> >
> > On 2012-08-14 10:07:54AM +0530, tarak karmakar wrote:
> >> Thanks for the quick reply, I have given this command to add 612 water
> >> molecules.
> >> genbox -cs spc216 -nmol 612 -cp ala_box.gro -o ala_solv.gro -p ala.top
> >>
> >> But in the solvated file, I see there are 668 water molecules.
> >> A part of the output while adding water molecules is as follows
> >>
> >>  Using plugin gro for structure file ala_solv.gro
> >> Info) Using plugin gro for coordinates from file ala_solv.gro
> >> Info) Determining bond structure from distance search ...
> >> Info) Finished with coordinate file ala_solv.gro.
> >> Info) Analyzing structure ...
> >> Info)Atoms: 2026
> >> Info)Bonds: 1357
> >> Info)Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0
> >> Info)Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0
> >> Info)Residues: 671
> >> Info)Waters: 668
> >> Warning) Unusual bond between residues:  1 (none) and 2 (protein)
> >> Warning) Unusual bond between residues:  2 (protein) and 3 (none)
> >> Info)Segments: 1
> >> Info)Fragments: 669   Protein: 1   Nucleic: 0
> >>
> >>
> >> On Tue, Aug 14, 2012 at 9:46 AM, Mark Abraham  
> >> wrote:
> >> > On 14/08/2012 2:02 PM, tarak karmakar wrote:
> >> >>
> >> >> Dear All,
> >> >>
> >> >> Is there any way to add a specific number of water ( let say 650
> >> >> water) molecules while dissolving the solute in a given box ?
> >> >
> >> >
> >> > Check out genbox -h
> >> >
> >> > Mark
> >> > --
> >> > gmx-users mailing listgmx-users@gromacs.org
> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> > * Only plain text messages are allowed!
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> > * Please don't pos

Re: [gmx-users] desired no of water molecules

[Peter C. Lai]

Did you have waters in the system before adding another 612?

I don't know how VMD counts waters, but another way is to grep -c for SOL in 
the resulting gro file and divide by 3.

On 2012-08-14 10:07:54AM +0530, tarak karmakar wrote:
> Thanks for the quick reply, I have given this command to add 612 water
> molecules.
> genbox -cs spc216 -nmol 612 -cp ala_box.gro -o ala_solv.gro -p ala.top
> 
> But in the solvated file, I see there are 668 water molecules.
> A part of the output while adding water molecules is as follows
> 
>  Using plugin gro for structure file ala_solv.gro
> Info) Using plugin gro for coordinates from file ala_solv.gro
> Info) Determining bond structure from distance search ...
> Info) Finished with coordinate file ala_solv.gro.
> Info) Analyzing structure ...
> Info)Atoms: 2026
> Info)Bonds: 1357
> Info)Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0
> Info)Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0
> Info)Residues: 671
> Info)Waters: 668
> Warning) Unusual bond between residues:  1 (none) and 2 (protein)
> Warning) Unusual bond between residues:  2 (protein) and 3 (none)
> Info)Segments: 1
> Info)Fragments: 669   Protein: 1   Nucleic: 0
> 
> 
> On Tue, Aug 14, 2012 at 9:46 AM, Mark Abraham  wrote:
> > On 14/08/2012 2:02 PM, tarak karmakar wrote:
> >>
> >> Dear All,
> >>
> >> Is there any way to add a specific number of water ( let say 650
> >> water) molecules while dissolving the solute in a given box ?
> >
> >
> > Check out genbox -h
> >
> > Mark
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Only plain text messages are allowed!
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 
> Tarak
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

[Peter C. Lai]

s. It is taken from the article Klauda, J. B. 
> > > >>>>>>> et al. 2010 J. Phys. Chem. B, 114, 7830-7843.
> > > >>>>>>>
> > > >>>>>>> At first, I tested normal TIP3P vs. CHARMM TIP3P and saw that 
> > > >>>>>>> normal TIP3P gives smaller Area per lipid of about 2-3 Angstroms. 
> > > >>>>>>> This was also observed by T.J. Piggot (personnal communication) 
> > > >>>>>>> and Tieleman (Sapay, N. et al. 2010 J. Comp. Chem. 32, 
> > > >>>>>>> 1400-1410). So, I will present only the simulations using CHARMM 
> > > >>>>>>> TIP3P. As in Klauda's paper, my simulations are at 310K and 1 
> > > >>>>>>> atm. As them, I used a switch cutoff for vdw, and I used normal 
> > > >>>>>>> cutoff for PME. The simulations are 20 ns. I can send my .mdp 
> > > >>>>>>> file for more details. I varied the switch condition on vdw :
> > > >>>>>>>
> > > >>>>>>> 1- For a switch from 0.8 to 1.2 (as in Klauda's paper), I got 
> > > >>>>>>> Area per lipid of about 56.5 Angstroms2; whereas they got 59.2 in 
> > > >>>>>>> their paper, matching the experimental value of 59.75-60.75.
> > > >>>>>>> 2- For a switch from 1.0 to 1.2, I got Area per lipid of about 
> > > >>>>>>> 53.5 Angstroms2, which is smaller than the previous cutoff. This 
> > > >>>>>>> is surprising since a previous thread on gromacs-users mailing 
> > > >>>>>>> lists said that increasing the lower cutoff, increased the Area 
> > > >>>>>>> per lipid or had not impact on POPC of DPPC.
> > > >>>>>>> 3- For a switch from 1.1 to 1.2, I got Area per lipid of about 55 
> > > >>>>>>> Angstroms2.
> > > >>>>>>> 4- For a hard cutoff at 1.4, I got Area per lipid of about 52 
> > > >>>>>>> Angstroms2.
> > > >>>>>>>
> > > >>>>>>> I also tried to re-equilibrate the membrane in the NPAT ensemble 
> > > >>>>>>> for 10 ns at 310K and 1 atm. Then, when I launched the simulation 
> > > >>>>>>> in NPT, I ended up with different results :
> > > >>>>>>>
> > > >>>>>>> 1- Switch from 0.8 to 1.2 gave a smaller area per lipid of 54 
> > > >>>>>>> Angstroms2.
> > > >>>>>>> 2- Switch from 1.0 to 1.2 gave a larger area per lipid of 55 
> > > >>>>>>> Angstroms2.
> > > >>>>>>> 4- Hard cutoff at 1.4 gave a similar area per lipid of 52.5 
> > > >>>>>>> Angstroms2.
> > > >>>>>>>
> > > >>>>>>> I looked at the POPE paramaters for CHARMM36 in Gromacs, and they 
> > > >>>>>>> agree with the published parameters.
> > > >>>>>>>
> > > >>>>>>> Am I doing anything wrong? Is their someone else experiencing a 
> > > >>>>>>> similar problem for POPE? If yes, how did you solved it?
> > > >>>>>>>
> > > >>>>>>> Should I instead use CHARMM27 parameters in the NPAT ensemble? I 
> > > >>>>>>> want to study the interaction between a peptide and the POPE 
> > > >>>>>>> membrane. I am troubled that the NPAT ensemble might influence my 
> > > >>>>>>> results in a bad way. Also, I can not use OPLS AA nor GROMOS for 
> > > >>>>>>> the protein interactions because these force fields are not 
> > > >>>>>>> giving the correct structural ensemble for my peptide in solution.
> > > >>>>>>>
> > > >>>>>>> I am willing to send more information if you need.
> > > >>>>>>>
> > > >>>>>>> Thanks a lot,
> > > >>>>>>> Sincerely,
> > > >>>>>>>
> > > >>>>>>> Sébastien --
> > > >>>>>>> gmx-users mailing list gmx-users@gromacs.org
> > > >>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > >>>>>>> * Only plain text 

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

[Peter C. Lai]

t; On 2012-07-20 09:46:13AM -0300, Sebastien Cote wrote:
> > > >>>>>>> Dear Gromacs users,
> > > >>>>>>>
> > > >>>>>>> My simulations on a POPE membrane using the CHARMM36 parameters 
> > > >>>>>>> are giving ''area per lipid'' values well below the experimental 
> > > >>>>>>> value (59.75-60.75 Angstroms2). Is their someone else 
> > > >>>>>>> experiencing a similar problem? If yes, how did you solved it?
> > > >>>>>>>
> > > >>>>>>> I did the following :
> > > >>>>>>>
> > > >>>>>>> I used the CHARMM36 parameters kindly provided by Thomas J. 
> > > >>>>>>> Piggot on the Users contribution section on Gromacs website.
> > > >>>>>>> My starting configuration was taken from : 
> > > >>>>>>> http://terpconnect.umd.edu/~jbklauda/research/download.html
> > > >>>>>>> It is a POPE membrane of 80 lipids equilibrated in NPT at T=310K 
> > > >>>>>>> and P=1atm for 40 ns. It is taken from the article Klauda, J. B. 
> > > >>>>>>> et al. 2010 J. Phys. Chem. B, 114, 7830-7843.
> > > >>>>>>>
> > > >>>>>>> At first, I tested normal TIP3P vs. CHARMM TIP3P and saw that 
> > > >>>>>>> normal TIP3P gives smaller Area per lipid of about 2-3 Angstroms. 
> > > >>>>>>> This was also observed by T.J. Piggot (personnal communication) 
> > > >>>>>>> and Tieleman (Sapay, N. et al. 2010 J. Comp. Chem. 32, 
> > > >>>>>>> 1400-1410). So, I will present only the simulations using CHARMM 
> > > >>>>>>> TIP3P. As in Klauda's paper, my simulations are at 310K and 1 
> > > >>>>>>> atm. As them, I used a switch cutoff for vdw, and I used normal 
> > > >>>>>>> cutoff for PME. The simulations are 20 ns. I can send my .mdp 
> > > >>>>>>> file for more details. I varied the switch condition on vdw :
> > > >>>>>>>
> > > >>>>>>> 1- For a switch from 0.8 to 1.2 (as in Klauda's paper), I got 
> > > >>>>>>> Area per lipid of about 56.5 Angstroms2; whereas they got 59.2 in 
> > > >>>>>>> their paper, matching the experimental value of 59.75-60.75.
> > > >>>>>>> 2- For a switch from 1.0 to 1.2, I got Area per lipid of about 
> > > >>>>>>> 53.5 Angstroms2, which is smaller than the previous cutoff. This 
> > > >>>>>>> is surprising since a previous thread on gromacs-users mailing 
> > > >>>>>>> lists said that increasing the lower cutoff, increased the Area 
> > > >>>>>>> per lipid or had not impact on POPC of DPPC.
> > > >>>>>>> 3- For a switch from 1.1 to 1.2, I got Area per lipid of about 55 
> > > >>>>>>> Angstroms2.
> > > >>>>>>> 4- For a hard cutoff at 1.4, I got Area per lipid of about 52 
> > > >>>>>>> Angstroms2.
> > > >>>>>>>
> > > >>>>>>> I also tried to re-equilibrate the membrane in the NPAT ensemble 
> > > >>>>>>> for 10 ns at 310K and 1 atm. Then, when I launched the simulation 
> > > >>>>>>> in NPT, I ended up with different results :
> > > >>>>>>>
> > > >>>>>>> 1- Switch from 0.8 to 1.2 gave a smaller area per lipid of 54 
> > > >>>>>>> Angstroms2.
> > > >>>>>>> 2- Switch from 1.0 to 1.2 gave a larger area per lipid of 55 
> > > >>>>>>> Angstroms2.
> > > >>>>>>> 4- Hard cutoff at 1.4 gave a similar area per lipid of 52.5 
> > > >>>>>>> Angstroms2.
> > > >>>>>>>
> > > >>>>>>> I looked at the POPE paramaters for CHARMM36 in Gromacs, and they 
> > > >>>>>>> agree with the published parameters.
> > > >>>>>>>
> > > >>>>>>> Am I doing anything wrong? Is their someone else experiencing a 
> > >

Re: [gmx-users] NVT equilibration

[Peter C. Lai]

On 2012-08-09 05:56:46AM -0700, Shima Arasteh wrote:
> Thanks for replies.
> 
> Some bonds are rotated more than 30 degrees ,as it's written just before 
> turning off the equilibration.
> Is this over-rotation also included in interaction with PBC images?

So the system crashed before LINCS did. Perhaps more energy minimization
would be helpful? See what atoms/residues were misbehaving (when LINCS
throws those errors, it gives you the atom #) and look at its neighbors to
see what sort of large forces might arise.

> 
> Am I supposed to change the rcoulomb and rvdw cutoffs? How would I be sure of 
> a correct changes? 
> 

You are supposed to use the cutoffs appropriate for your forcefield.

> 
> Sincerely,
> Shima
> 
> 
> - Original Message -
> From: Peter C. Lai 
> To: Discussion list for GROMACS users 
> Cc: 
> Sent: Thursday, August 9, 2012 5:08 PM
> Subject: Re: [gmx-users] NVT equilibration
> 
> Parts of your system shifted too much (in Y dimension) for PME to handle.
> 
> What happens to the system up to the point of the crash?
> 
> How large is the system (particle count) vs. # of PME nodes used?
> Could be your system is too small for the # of PME nodes used
> 
> Is the protein somehow interacting with its own PBC images? Is there enough
> water in the box to shield the protein from seeing itself in the next box
> over - it's probably safe to go with a thickness of water around the protein
> that is equal to the rcoulomb and rvdw cutoffs (that way you really get 2x
> the distance between protein images).
> 
> 
> On 2012-08-09 05:23:17AM -0700, Shima Arasteh wrote:
> > Dear gmx users,
> > 
> > I used the NVT (T=300) equilibration for my system ( a protein in water). 
> > The first time, I set 100 ps for system for equilibration, It resulted in 
> > RMSD=3.96 with an average temperature around 299.803 K. 
> > 
> > Then I though of a better convergence, so set the equilibration to 200 ps. 
> > But it stopped due to some error:
> > Fatal error:
> > 1 particles communicated to PME node 4 are more than 2/3 times the cut-off 
> > out of the domain decomposition cell of their charge group in dimension y.
> > This usually means that your system is not well equilibrated.
> > 
> > 
> > I'd like to know why such an error might happen? Is a shorter equilibration 
> > better for NVT generally? 
> > 
> > 
> > Cheers,
> > Shima
> > -- 
> > gmx-users mailing list    gmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Only plain text messages are allowed!
> > * Please search the archive at 
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
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> 
> -- 
> ==
> Peter C. Lai            | University of Alabama-Birmingham
> Programmer/Analyst        | KAUL 752A
> Genetics, Div. of Research    | 705 South 20th Street
> p...@uab.edu            | Birmingham AL 35294-4461
> (205) 690-0808            |
> ==
> 
> -- 
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==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] NVT equilibration

[Peter C. Lai]

Parts of your system shifted too much (in Y dimension) for PME to handle.

What happens to the system up to the point of the crash?

How large is the system (particle count) vs. # of PME nodes used?
Could be your system is too small for the # of PME nodes used

Is the protein somehow interacting with its own PBC images? Is there enough
water in the box to shield the protein from seeing itself in the next box
over - it's probably safe to go with a thickness of water around the protein
that is equal to the rcoulomb and rvdw cutoffs (that way you really get 2x
the distance between protein images).


On 2012-08-09 05:23:17AM -0700, Shima Arasteh wrote:
> Dear gmx users,
> 
> I used the NVT (T=300) equilibration for my system ( a protein in water). The 
> first time, I set 100 ps for system for equilibration, It resulted in 
> RMSD=3.96 with an average temperature around 299.803 K. 
> 
> Then I though of a better convergence, so set the equilibration to 200 ps. 
> But it stopped due to some error:
> Fatal error:
> 1 particles communicated to PME node 4 are more than 2/3 times the cut-off 
> out of the domain decomposition cell of their charge group in dimension y.
> This usually means that your system is not well equilibrated.
> 
> 
> I'd like to know why such an error might happen? Is a shorter equilibration 
> better for NVT generally? 
> 
> 
> Cheers,
> Shima
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
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-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

[Peter C. Lai]

0300, Sebastien Cote wrote:
> >>>>>>> Dear Gromacs users,
> >>>>>>>
> >>>>>>> My simulations on a POPE membrane using the CHARMM36 parameters are 
> >>>>>>> giving ''area per lipid'' values well below the experimental value 
> >>>>>>> (59.75-60.75 Angstroms2). Is their someone else experiencing a 
> >>>>>>> similar problem? If yes, how did you solved it?
> >>>>>>>
> >>>>>>> I did the following :
> >>>>>>>
> >>>>>>> I used the CHARMM36 parameters kindly provided by Thomas J. Piggot on 
> >>>>>>> the Users contribution section on Gromacs website.
> >>>>>>> My starting configuration was taken from : 
> >>>>>>> http://terpconnect.umd.edu/~jbklauda/research/download.html
> >>>>>>> It is a POPE membrane of 80 lipids equilibrated in NPT at T=310K and 
> >>>>>>> P=1atm for 40 ns. It is taken from the article Klauda, J. B. et al. 
> >>>>>>> 2010 J. Phys. Chem. B, 114, 7830-7843.
> >>>>>>>
> >>>>>>> At first, I tested normal TIP3P vs. CHARMM TIP3P and saw that normal 
> >>>>>>> TIP3P gives smaller Area per lipid of about 2-3 Angstroms. This was 
> >>>>>>> also observed by T.J. Piggot (personnal communication) and Tieleman 
> >>>>>>> (Sapay, N. et al. 2010 J. Comp. Chem. 32, 1400-1410). So, I will 
> >>>>>>> present only the simulations using CHARMM TIP3P. As in Klauda's 
> >>>>>>> paper, my simulations are at 310K and 1 atm. As them, I used a switch 
> >>>>>>> cutoff for vdw, and I used normal cutoff for PME. The simulations are 
> >>>>>>> 20 ns. I can send my .mdp file for more details. I varied the switch 
> >>>>>>> condition on vdw :
> >>>>>>>
> >>>>>>> 1- For a switch from 0.8 to 1.2 (as in Klauda's paper), I got Area 
> >>>>>>> per lipid of about 56.5 Angstroms2; whereas they got 59.2 in their 
> >>>>>>> paper, matching the experimental value of 59.75-60.75.
> >>>>>>> 2- For a switch from 1.0 to 1.2, I got Area per lipid of about 53.5 
> >>>>>>> Angstroms2, which is smaller than the previous cutoff. This is 
> >>>>>>> surprising since a previous thread on gromacs-users mailing lists 
> >>>>>>> said that increasing the lower cutoff, increased the Area per lipid 
> >>>>>>> or had not impact on POPC of DPPC.
> >>>>>>> 3- For a switch from 1.1 to 1.2, I got Area per lipid of about 55 
> >>>>>>> Angstroms2.
> >>>>>>> 4- For a hard cutoff at 1.4, I got Area per lipid of about 52 
> >>>>>>> Angstroms2.
> >>>>>>>
> >>>>>>> I also tried to re-equilibrate the membrane in the NPAT ensemble for 
> >>>>>>> 10 ns at 310K and 1 atm. Then, when I launched the simulation in NPT, 
> >>>>>>> I ended up with different results :
> >>>>>>>
> >>>>>>> 1- Switch from 0.8 to 1.2 gave a smaller area per lipid of 54 
> >>>>>>> Angstroms2.
> >>>>>>> 2- Switch from 1.0 to 1.2 gave a larger area per lipid of 55 
> >>>>>>> Angstroms2.
> >>>>>>> 4- Hard cutoff at 1.4 gave a similar area per lipid of 52.5 
> >>>>>>> Angstroms2.
> >>>>>>>
> >>>>>>> I looked at the POPE paramaters for CHARMM36 in Gromacs, and they 
> >>>>>>> agree with the published parameters.
> >>>>>>>
> >>>>>>> Am I doing anything wrong? Is their someone else experiencing a 
> >>>>>>> similar problem for POPE? If yes, how did you solved it?
> >>>>>>>
> >>>>>>> Should I instead use CHARMM27 parameters in the NPAT ensemble? I want 
> >>>>>>> to study the interaction between a peptide and the POPE membrane. I 
> >>>>>>> am troubled that the NPAT ensemble might influence my results in a 
> >>>>>>> bad way. Also, I can not use OPLS AA nor GROMOS for the protein 
> >>>>>>> interactions because these

Re: [gmx-users] GROMACS OR NAMD

[Peter C. Lai]

Among simulation people at my institution, all the other lipids people
use NAMD. This was mostly a user-experience decision. When they started
their work, NAMD had better parallelization (this was before Gromacs 4+ 
came out). Now even though Gromacs has great parallelization, they don't
see a reason to switch to Gromacs because they like retaining a more "plug and
play" type of experience; although from a science perspective, this raises
questions about how rigorous they have validated their setups over time.

When you have a frontend like VMD that ties directly into NAMD job submission,
a lot of people like that, instead of tweaking all the parameters by hand.

However, NAMD isn't entirely opensource, at least not like Gromacs is (you
have to sign an EULA to use NAMD). For some people that can also be an
issue (if they are programmers do they want to be beholden to University of 
Illinois intellectual property management if they want to access or modify
the NAMD source code?)

The Formula 1 (or kit car) vs. station wagon (I guess nowadays it's all about 
minivans and crossover SUVs, isn't it? :) analogy is pretty apropos for the 
comparison between Gromacs and NAMD, respectively.

On 2012-07-27 11:20:54AM -0400, Justin Lemkul wrote:
> 
> 
> On 7/27/12 10:58 AM, Shima Arasteh wrote:
> > Thanks dear Mark for your reply.
> > It was just a simple question, liked to hear answers from the one who knows 
> > more about the simulation packages more than me. Again thanks dear Mark.
> >
> > In my own, I've only worked with GROMACS and don't have any experiences of 
> > NAMD.
> >
> > About the problem which I want to define by simulation (simulation of a 
> > protein in lipid bilayer and studying its ion conduction) , both NAMD and 
> > GROMACS are applied but I've not got the real advantages of any one over 
> > the other.
> > If anybody knows an advantageous article in this about would be appreciated 
> > if suggests me.
> 
> I doubt such a thing exists, as there are no universal standards for what 
> makes 
> one simulation package better than another.  As Mark said, it is really 
> user-dependent.  That requires you to read the respective manuals for what 
> features and optimizations may be available.  Assuming that either simulation 
> package has the algorithms you need, then the choice comes down to which 
> package 
> you find easier to use and which may make best use of the available hardware, 
> which may require you to reach out to cluster sysadmins for advice.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
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Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

[Peter C. Lai]

actions 
> > > because these force fields are not giving the correct structural ensemble 
> > > for my peptide in solution.
> > >
> > > I am willing to send more information if you need.
> > >
> > > Thanks a lot,
> > > Sincerely,
> > >
> > > Sébastien --
> > > gmx-users mailing list gmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
> > --
> > ==
> > Peter C. Lai | University of Alabama-Birmingham
> > Programmer/Analyst | KAUL 752A
> > Genetics, Div. of Research | 705 South 20th Street
> > p...@uab.edu | Birmingham AL 35294-4461
> > (205) 690-0808 |
> > ==
> >
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Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

[Peter C. Lai]

Did you play with DispCorr?

On 2012-07-20 09:46:13AM -0300, Sebastien Cote wrote:
> 
> Dear Gromacs users,
>  
> My simulations on a POPE membrane using the CHARMM36 parameters are giving 
> ''area per lipid'' values well below the experimental value (59.75-60.75 
> Angstroms2). Is their someone else experiencing a similar problem? If yes, 
> how did you solved it? 
> 
> I did the following :
> 
> I used the CHARMM36 parameters kindly provided by Thomas J. Piggot on the 
> Users contribution section on Gromacs website.
> My starting configuration was taken from 
> : http://terpconnect.umd.edu/~jbklauda/research/download.html
> It is a POPE membrane of 80 lipids equilibrated in NPT at T=310K and P=1atm 
> for 40 ns. It is taken from the article Klauda, J. B. et al. 2010 J. Phys. 
> Chem. B, 114, 7830-7843.
> 
> At first, I tested normal TIP3P vs. CHARMM TIP3P and saw that normal TIP3P 
> gives smaller Area per lipid of about 2-3 Angstroms. This was also observed 
> by T.J. Piggot (personnal communication) and Tieleman (Sapay, N. et al. 2010 
> J. Comp. Chem. 32, 1400-1410). So, I will present only the simulations using 
> CHARMM TIP3P. As in Klauda's paper, my simulations are at 310K and 1 atm. As 
> them, I used a switch cutoff for vdw, and I used normal cutoff for PME. The 
> simulations are 20 ns. I can send my .mdp file for more details. I varied the 
> switch condition on vdw : 
>  
> 1- For a switch from 0.8 to 1.2 (as in Klauda's paper), I got Area per lipid 
> of about 56.5 Angstroms2; whereas they got 59.2 in their paper, matching the 
> experimental value of 59.75-60.75. 
> 2- For a switch from 1.0 to 1.2, I got Area per lipid of about 53.5 
> Angstroms2, which is smaller than the previous cutoff. This is surprising 
> since a previous thread on gromacs-users mailing lists said that increasing 
> the lower cutoff, increased the Area per lipid or had not impact on POPC of 
> DPPC. 
> 3- For a switch from 1.1 to 1.2, I got Area per lipid of about 55 Angstroms2. 
> 4- For a hard cutoff at 1.4, I got Area per lipid of about 52 Angstroms2.  
> 
> I also tried to re-equilibrate the membrane in the NPAT ensemble for 10 ns at 
> 310K and 1 atm. Then, when I launched the simulation in NPT, I ended up with 
> different results :
> 
> 1- Switch from 0.8 to 1.2 gave a smaller area per lipid of 54 Angstroms2.
> 2- Switch from 1.0 to 1.2 gave a larger area per lipid of 55 Angstroms2. 
> 4- Hard cutoff at 1.4 gave a similar area per lipid of 52.5 Angstroms2.
> 
> I looked at the POPE paramaters for CHARMM36 in Gromacs, and they agree with 
> the published parameters.
> 
> Am I doing anything wrong? Is their someone else experiencing a similar 
> problem for POPE? If yes, how did you solved it?
> 
> Should I instead use CHARMM27 parameters in the NPAT ensemble? I want to 
> study the interaction between a peptide and the POPE membrane. I am troubled 
> that the NPAT ensemble might influence my results in a bad way. Also, I can 
> not use OPLS AA nor GROMOS for the protein interactions because these force 
> fields are not giving the correct structural ensemble for my peptide in 
> solution. 
> 
> I am willing to send more information if you need. 
> 
> Thanks a lot, 
> Sincerely,
> 
> Sébastien   -- 
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Re: [gmx-users] Some interactions seem to be assigned multiple times

[Peter C. Lai]

Did the RTP file include new atoms/interactions (angles, dihedrals)? If not 
then I don't know. If it did, then you should check to make sure you don't
have the same interactions defined in the .itp files.

On 2012-07-20 09:02:56AM -0700, Shima Arasteh wrote:
> 
> 
>  May this error happen because of the incorrect value of a new-defined 
> residue in .rtp file? 
> 
> 
> 
> Sincerely,
> Shima
> 
> 
> ----- Original Message -
> From: Peter C. Lai 
> To: gmx-users@gromacs.org
> Cc: 
> Sent: Wednesday, July 18, 2012 9:00 AM
> Subject: Re: [gmx-users] Some interactions seem to be assigned multiple times
> 
> and this did not happen with EM?
> 
> Did you add new atoms/FF parameters to the existing C36 set?
> 
> On 2012-07-13 02:05:47AM -0700, Shima Arasteh wrote:
> > 
> > Dear gmx users,
> > 
> > 
> > My system is composed of a protein and water. I am working with CHARMM36 
> > and the current version of Gromacs, 4.5.5.
> > For NVT equilibration , I get this error:
> > 
> > "Software inconsistency error:
> >  Some interactions seem to be assigned multiple times"
> > 
> > 
> > Through the mailing list, I just found that some bugs might be the reason 
> > of the error, and the Gromacs version should be current. But as I said I 
> > use the current version of Gromacs. I really don't have any idea for 
> > solving this problem.
> > 
> > Any suggestions would be appreciated.
> > 
> > 
> > Sincerely,
> > Shima
> > -- 
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> -- 
> ==
> Peter C. Lai            | University of Alabama-Birmingham
> Programmer/Analyst        | KAUL 752A
> Genetics, Div. of Research    | 705 South 20th Street
> p...@uab.edu            | Birmingham AL 35294-4461
> (205) 690-0808            |
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Genetics, Div. of Research  | 705 South 20th Street
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Re: [gmx-users] Some interactions seem to be assigned multiple times

[Peter C. Lai]

and this did not happen with EM?

Did you add new atoms/FF parameters to the existing C36 set?

On 2012-07-13 02:05:47AM -0700, Shima Arasteh wrote:
> 
> Dear gmx users,
> 
> 
> My system is composed of a protein and water. I am working with CHARMM36 and 
> the current version of Gromacs, 4.5.5.
> For NVT equilibration , I get this error:
> 
> "Software inconsistency error:
>  Some interactions seem to be assigned multiple times"
> 
> 
> Through the mailing list, I just found that some bugs might be the reason of 
> the error, and the Gromacs version should be current. But as I said I use the 
> current version of Gromacs. I really don't have any idea for solving this 
> problem.
> 
> Any suggestions would be appreciated.
> 
> 
> Sincerely,
> Shima
> -- 
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
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(205) 690-0808  |
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Re: [gmx-users] sovation with tip3p

[Peter C. Lai]

This is not really true. It is perfectly appropriate to use spc216.gro with 
the tip3p water model since any spacing differences will settle out during
npt equilibration anyway.

On 2012-07-11 02:28:52PM +0430, amir abbasi wrote:
> Hi,
> I had this problem too.
> unfortunately gmx not included tip3p model of water anymore.
> You have two ways.
> 1.using spc216 that gmx offers or
> 2.Buil your system in Ambertools (leap) and convert your .prmtop and
> .inpcrd files to .top and .gro
> if you persist on using tip3p water model i suggest you to pick second way.
> Regards,
> Amir
> 
> 
> Subject: [gmx-users] sovation with tip3p
> 
> Hi all,
> 
> I'm going to do the step 3 in Justin's tutorial (Lysozyme in water) .
> In this step, the solvation is accomplished through this command:
> genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
> 
> in which that spc216.gro is used. In first step I had used the TIP3P
> water model, here I'd rather to call TIP3P too. But there is not
> tip3p.gro in share/top .
> 
> I would appreciate you if you give me any suggestion.
> Thanks in advance.
> 
> 
> 
> 
> Sincerely,
> Shima
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Genetics, Div. of Research  | 705 South 20th Street
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Re: [gmx-users] water model

[Peter C. Lai]

For CHARMM the typical water model is TIP3P, although I tend to use TIPS3P
since it's been reported on the mailing list to give better interactions with 
bilayers. (Also easier to pass by picky reviewers at the expense of ns/day,
obviously).

The following thread may be helpful too:
http://lists.gromacs.org/pipermail/gmx-users/2010-September/053960.html

On 2012-07-09 10:49:57AM -0700, Shima Arasteh wrote:
> 
> 
>  Dear gmx friends,
> 
> Is there the best water model for each force fields? Which options are 
> supposed to be noticed in applying the best water model.
> I need to tell you that I apply C36 in my simulations.
> 
> Thanks in advance.
> 
> Sincerely,
> Shima
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Genetics, Div. of Research  | 705 South 20th Street
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(205) 690-0808  |
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Re: [gmx-users] How to assign charge group for ester?

[Peter C. Lai]

You neglected to mention what Force Field you are using.

See Also: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060752.html

On 2012-07-03 10:47:25AM -0400, zifeng li wrote:
> Dear users,
> 
> I use gromacs version 4.5.4 and is building residues of my own polymer which
> has a ester group (COOR). Should I consider the ester as one neutral
> group or split it into two groups( -COO and -R) ?
> 
> Here's some information I find:
> 
> 1. Should consider them as one group. Based on the fact that Gromacs
> consider a charge group to be a particle so that if I make a
> non-neutral charge group, the total charge within a verlet list might
> not be 0 if
> these two groups are not included in a list at the same time.
> 
> 2. Should split into two groups. First, on Gromacs website, it is said
> the charge group usually includes 4 or less atoms. Second,
> in aminoacids.rtp file, I find some aminoacids, like Asn, which do
> have a non-neutral charge group.
> 
> Would this make a difference?
> 
> Thanks in advance,
> 
> -Zifeng
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Genetics, Div. of Research  | 705 South 20th Street
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(205) 690-0808  |
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Re: [gmx-users] Berger lipid

[Peter C. Lai]

323 is proper for a higher melting point lipid like DPPC. You can easily 
simulate POPC at 300, and many other people have done so.  In fact I received 
criticism from a reviewer as to why I picked an elevated temperature of 310, 
despite the fact that 310 is physiological temperature (to make some 
experimentalist reviewers happy). Some early rhodopsin runs were done at
310 and I'm pretty sure that was included as a reference in the rationale
for the elevated temperature (besides the standard "310 is well above the
solid phase transition temperature for POPC" line). Neither the g_membed
authors nor Klauda run POPC above 310K if I remember correctly.

On 2012-06-30 07:33:38AM -0700, Shima Arasteh wrote:
> Dear Peter,
> Thanks for your link and the article.
> I'd like to know more about your paper. You've mentioned in it that the 
> temperature of POPC equilibrated, is 310 K. As I saw in Justin's tutorial , 
> 323 K is proper, however it was a different system simulated and also many 
> parameters are not the same as your system . Would you telling me about the 
> reason of 310 K?
> 
> Thanks in advance
> 
>  
> Sincerely,
> Shima
> 
> 
> - Original Message -
> From: Peter C. Lai 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Cc: 
> Sent: Friday, June 29, 2012 2:54 PM
> Subject: Re: [gmx-users] Berger lipid
> 
> yes
> http://www.frontiersin.org/Bioinformatics_and_Computational_Biology/10.3389/fgene.2012.00061/abstract
> 
> The files are here:
> http://uab.hyperfine.info/~pcl/files/popc36/
> 
> On 2012-06-28 09:58:26PM -0700, Shima Arasteh wrote:
> > Yes, I remember now...you are right :) But I didn't know 
> > the linked you sent me, was your own output! However  I wanted to know if 
> > it is necessary to produce the .itp file on my own or not.
> > 
> > I still have this link, so will cite to you. It would be a good idea to see 
> > its package in lipidbook too.
> > Thanks Peter
> > 
> > 
> > 
> > 
> > Sincerely,
> > Shima
> > 
> > 
> > 
> > From: Peter Lai 
> > To: Discussion list for GROMACS users  
> > Sent: Friday, June 29, 2012 7:14 AM
> > Subject: RE: [gmx-users] Berger lipid
> > 
> > Uh didn't we go through all of this like more than a month ago? I published 
> > a paper using C36 POPC and even a linked to my popc.itp for it on this 
> > list...
> > 
> > Of course Shima is welcome to pdb2gmx his own POPC, which I am fairly 
> > certain will result in an identical file...
> > 
> > Lipidbook seems to only have C36 POPE. I guess maybe I will upload ours.
> > 
> > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on 
> > behalf of Justin A. Lemkul [jalem...@vt.edu]
> > Sent: Thursday, June 28, 2012 7:56 PM
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] Berger lipid
> > 
> > On 6/28/12 8:54 PM, Shima Arasteh wrote:
> > > Yes, I know that as studied the Kalp15 tutorial.
> > > Sorry, the last question :)
> > > :
> > >
> > >    DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is 
> > >it ok?  Because I see that POPC.itp is also required for simulation of 
> > >protein in bilayer.
> > >
> > 
> > You need a topology of some sort.  It depends on what parameters you have on
> > hand.  If you do not have popc.itp from anywhere, then you need to generate 
> > it
> > somehow.  If it is present in the .rtp file for CHARMM36 that you have, 
> > then you
> > can run pdb2gmx on it.
> > 
> > -Justin
> > 
> > --
> > 
> > 
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > 
> > 
> > 
> > 
> > --
> > gmx-users mailing list    gmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > gmx-users mailin

Re: [gmx-users] Berger lipid

[Peter C. Lai]

yes
http://www.frontiersin.org/Bioinformatics_and_Computational_Biology/10.3389/fgene.2012.00061/abstract

The files are here:
http://uab.hyperfine.info/~pcl/files/popc36/

On 2012-06-28 09:58:26PM -0700, Shima Arasteh wrote:
> Yes, I remember now...you are right :) But I didn't know the 
> linked you sent me, was your own output! However  I wanted to know if it is 
> necessary to produce the .itp file on my own or not.
> 
> I still have this link, so will cite to you. It would be a good idea to see 
> its package in lipidbook too.
> Thanks Peter
> 
> 
> 
> 
> Sincerely,
> Shima
> 
> 
> 
> From: Peter Lai 
> To: Discussion list for GROMACS users  
> Sent: Friday, June 29, 2012 7:14 AM
> Subject: RE: [gmx-users] Berger lipid
> 
> Uh didn't we go through all of this like more than a month ago? I published a 
> paper using C36 POPC and even a linked to my popc.itp for it on this list...
> 
> Of course Shima is welcome to pdb2gmx his own POPC, which I am fairly certain 
> will result in an identical file...
> 
> Lipidbook seems to only have C36 POPE. I guess maybe I will upload ours.
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
> of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Thursday, June 28, 2012 7:56 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Berger lipid
> 
> On 6/28/12 8:54 PM, Shima Arasteh wrote:
> > Yes, I know that as studied the Kalp15 tutorial.
> > Sorry, the last question :)
> > :
> >
> >    DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is it 
> >ok?  Because I see that POPC.itp is also required for simulation of protein 
> >in bilayer.
> >
> 
> You need a topology of some sort.  It depends on what parameters you have on
> hand.  If you do not have popc.itp from anywhere, then you need to generate it
> somehow.  If it is present in the .rtp file for CHARMM36 that you have, then 
> you
> can run pdb2gmx on it.
> 
> -Justin
> 
> --
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> 
> 
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-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] no SOL in topology file after genbox command

[Peter C. Lai]

Make sure your top file #include ff/spc.itp

On 2012-06-29 11:35:24AM +0200, reising...@rostlab.informatik.tu-muenchen.de 
wrote:
> Hi everybody,
> I wanted to add water in the box where I put the protein with the command
> 
> genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro
> 2>>logErr 1>>logOut
> 
> The result is that I have indeed water (SOL) in the protein file
> (3m71_water.gro). But there is a problem in the topology file (3m71.top).
> Here I only have the line in the end after [ molecules ] where it is
> written how many SOL were added to the structure:
> 
> SOL 14329
> 
> But in the [ moleculetype ] part of the topology file there is no SOL
> mentioned. This causes an error when I want to call grompp.
> 
> SO my question is: why is there no SOL in the [ moleculetype ] part?
> 
> Best, Eva
> 
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==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] Insertion protein in the membrane via G_membed

[Peter C. Lai]

My suggestion is to either add the ligand back in after g_membed removes it 
or to not g_membed the system with the ligand, if it is acceptable. (Is your
ligand supposed to interact with the bilayer in any meaningful way?)

Or don't use g_membed and fall back to inflatgro for insertion.

On 2012-06-20 12:40:30PM +0400, James Starlight wrote:
> But where exactly error in such inclussion ?
> 
> In G_membed manual I've found only this statement about inclussion of the
> ligands
> 
> When the group to embed is not a default group, such as a protein and
> its crystal water, an ndx file
> should also be provided to g membed. Make sure all the molecule types in
> the group to embed are unique,
> e.g. the molecule type of the crystal waters should be different from that
> of the solvent. Also the freeze
> and energy exclusion parameters in the mdp file should be changed to match
> the name of the group to
> embed.
> 
> This tell nothing how exactly define mdp file. The way that I've used gave
> me those strange error that pop ( membrane ) was in the first group wich
> really contained of only merged protein and ligand (2 different mol.
> types). This merging I've done by means of index_ndx based on the GRO file
> with I've provide to GROMPP.
> 
> Also I've tried to do it in another manner defining all groups separately
> 
> integrator = md
> energygrps  = Protein ADN
> freezegrps = Protein ADN
> freezedim  = Y Y Y Y Y Y
> energygrp_table
> energygrp_excl = Protein Protein
> 
> In that case I have no such problem but during insertion G_membed has
> deleted ADN.
> 
> James
> 
> 
> 
> 2012/6/20 Mark Abraham 
> 
> > On 20/06/2012 5:08 PM, James Starlight wrote:
> >
> >> Mark,
> >>
> >> I've made changes in the input mdp file
> >>
> >> integrator = md
> >> energygrps  = Protein_ADN
> >> freezegrps = Protein_ADN
> >> freezedim  = Y Y Y
> >> energygrp_table
> >> energygrp_excl = Protein_ADN Protein_ADN
> >>
> >> here Protein_ADN is the protein_ligand defined in the index.mdp
> >>
> >> than I've processed by grompp without problems
> >>
> >> but during insertion step by follow command
> >> g_membed -f input.tpr -p topol.top -n index.ndx -xyinit 0.1 -xyend 1.0
> >> -nxy 1000
> >>
> >> here I choose Protein_ADN as the group to be inserted and POP as the
> >> group wich are membrane. Eventually I've obtained another strange error
> >>
> >> Moleculetype POP is found both in the group to insert and the rest of the
> >> system.
> >> Because we need to exclude all interactions between the atoms in the
> >> group to
> >> insert, the same moleculetype can not be used in both groups. Change the
> >> moleculetype of the molecules POP in the inserted group.
> >>
> >> I've checked my index.ndx and didt not find POP group in my first
> >> Protein_ADN group. Why this error should be ?
> >>
> >
> > Then it seems you're checking things that don't match each other. The
> > numbers in the index file must relate to the whole system, defined by the
> > [molecules] section. You need to make the index group from a file that
> > corresponds to that section, i.e. from the coordinate file you give to
> > grompp, which also must match that section. You should note also any
> > particular requirements in the g_membed documentation about whether the
> > insertion group has to be a single molecule or moleculetype.
> >
> > Mark
> >
> > --
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