[gmx-users] Re: Anomaly in Temperature Behavior

[Andrey Frolov]

S. Alireza B wrote
> During this run we freeze the solid phase in
> all three dimensions. We then take the final configuration of this run,
> unfreeze the solid phase, and subject it to a long NVE simulation to study
> the dissociation of the solid phase...
> 
> ... the temperature keeps increasing which is contrary to the physical
> fact that the dissociation
> process is endothermic.

1) Imagine you have just the solid state at the beginning of the simulation,
which is frozen (no forces are acting on the atoms). Then you unfreeze the
system, which means you switch on interactions between particles => non-zero
forces acting on particles appear. Despite the fact that the initial
velocities were zero, the non-zero forces in few integration time steps will
result in non-zero velocities on the particles, which means that temperature
will increase. So, to my mind, what you observe is not an anomaly. The solid
state in your NVE simulation is far from equilibrium. The quick increase of
temperature (in ~ 0.5 ps) is due to relaxation of the solid internal degrees
of freedom. I would expect, that no molecules melt to liquid phase in this
short time. Probably, you should just wait longer until solid starts melting
?

2) Also, I would suggest to prepare your system closer to equilibrium.
Instead of "freeze" you can use "position_restraints". Also, you can use
different  temperature coupling bathes to your solid and liquid. Setting
sufficiently lower reference temperature for the solid phase will prevent it
from melting.

3) Another suggestion, could it be that there is a spontaneous
crystallization in your system instead of melting ?

Andrey
 
Andrey I. Frolov, PhD 
Postdoctoral fellow 
Institute of Solution Chemistry 
Russian Academy of Sciences 




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[gmx-users] Re: help with building DNA in gromacs

[Justin Lemkul]

On 1/22/13 2:02 PM, Tom wrote:

Thanks a lot, Justin!

I names residue names to match the force field's expectations
But I am still having problem of using amber03.ff.
This my pdb file:
_
.
ATOM 28  H5DC5   1   2.443  -4.389   1.332  1.00  0.00   H
*ATOM 29  P DC2   7.171  -5.306   6.616  1.00  0.00   P 
*
ATOM 30  OP1   DC2   5.787  -5.066   7.086  1.00  0.00   O

__

When I pdb2gmx, i got Fatal error and choose 1: ( 1: AMBER03 protein, nucleic
AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003))
---
Atom P in residue DC 2 was not found in rtp entry*DC5 *with 28 atoms
while sorting atoms.
  error report
-

It seems gmx can not recognize the residue type DC and still used DC5 for 
residue 2.
Is there a way to solve this problem?



Please post a link to where the .pdb file can be downloaded.

Also, please do not reply to the entire digest.  The archive is already 
hopelessly confusing, but let's not make it any worse.


-Justin

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Virginia Tech
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Re: [gmx-users] Heme group with CHARMM27 FF

[Arvind Kannan]

For the benefit of anyone who happens to be Googling the same problem, the 
following lines inserted into the aminoacids.hdb file will tell pdb2gmx how to 
correctly protonate the heme.

HEME16
1   1   HA  CHA C1A C4D
1   1   HB  CHB C4A C1B
1   1   HC  CHC C4B C1C
1   1   HD  CHD C4C C1D
3   4   HMA CMA C3A C4A
2   6   HAA CAA CBA C2A
2   6   HBA CBA CGA CAA
3   4   HMB CMB C2B C1B
1   1   HAB CAB C3B CBB
2   3   HBB CBB CAB C3B
3   4   HMC CMC C2C C1C
1   1   HAC CAC C3C CBC
2   3   HBC CBC CAC C3C
3   4   HMD CMD C2D C1D
2   6   HAD CAD CBD C3D
2   6   HBD CBD CGD CAD

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Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian

[Christoph Junghans]

> Message: 5
> Date: Tue, 22 Jan 2013 19:42:01 +0100
> From: Szil?rd P?ll 
> Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on
> Debian
> To: Discussion list for GROMACS users 
> Message-ID:
> 
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Tue, Jan 22, 2013 at 12:45 PM, James Starlight 
> wrote:
>
>> Szilárd,
>>
>> Today I've tried to re-install cuda+gromacs and do apt-get
>> distr-upgrade but the same error was obtained during gromacs
>>
>
> I'm don't see how does the distribution upgrade relate to the issues you
> had (except if you have updated glibs to a newer version which is *still*
> incompatible with libcuda. You should probably try getting a more recent
> glibc and GCC version, one that libcuda is linked against. However, I'm not
> sure what the source of your problem is, so I can't suggest a certain
> solution.
I had a similar problem on Gentoo Linux
(https://bugs.gentoo.org/show_bug.cgi?id=452386), it helped to use a
newer version of gcc (>=4.6).

Cheers,

Christoph
>
>> compilation. By the way where I could provide --add-needed option ?
>
> CMAKE_EXE_LINKER_FLAGS=-wl,--add-needed
>
> Cheers,
> Szilárd
>
>
>>
>>
>> James
>>
>>
>> 2013/1/21 Szilárd Páll :
>> > Szilárd
>> --
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[gmx-users] Problems with g_anaeig

[James Starlight]

Dear Gromacs users!


There is some bug  with g_anaeig the souce of which I could not fully
understand.   I have problems when I perform PCA of X-ray data set.
Below you can my workflow.


g_covar -f b2ar_xray_coors.pdb  -s ref.pdb  -o PCA_eigenval.xvg -v
PCA_eigenvec.trr -av PCA_average.pdb -last 8
g_anaeig -v PCA_eigenvec.trr -s ref.pdb  -f b2ar_xray_coors.pdb -rmsf
eigrmsfPCA.xvg -filt


here b2ar_xray_coors.pdb  is the trajectory made from 10 X-ray
structures of my protein (only main chain atoms are included)
ref_pdb is the first frame of that trajectory


As the result I've obtained reasonable eigenvalues and aigenvectors
from g_covar BUT when I check filter trajectory ( produced by
g_anaeig) fitted it to the ref.pdb or to the averaged structure in
both cases I've obtained very distorted geometry of the  protein in
thefiltered trajectory. I have no such problems in case of PCA of MD
trajectory ( when  -f trajectory.trr is from the md snapshots not from
x-ray structures)


How it could be fixed ?


James
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Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian

[James Starlight]

Szilárd,

thanks for suggestion. Indeed I've noticed that versions of all
packages in classic debian are older in comparison to debian mint (
despite I've done maximum upgrade of the system via apt). Tomorrow
I'll try to install newest gcc and glibc and re-install gromacs.


James

2013/1/22 Szilárd Páll :
> On Tue, Jan 22, 2013 at 12:45 PM, James Starlight 
> wrote:
>
>> Szilárd,
>>
>> Today I've tried to re-install cuda+gromacs and do apt-get
>> distr-upgrade but the same error was obtained during gromacs
>>
>
> I'm don't see how does the distribution upgrade relate to the issues you
> had (except if you have updated glibs to a newer version which is *still*
> incompatible with libcuda. You should probably try getting a more recent
> glibc and GCC version, one that libcuda is linked against. However, I'm not
> sure what the source of your problem is, so I can't suggest a certain
> solution.
>
>> compilation. By the way where I could provide --add-needed option ?
>
> CMAKE_EXE_LINKER_FLAGS=-wl,--add-needed
>
> Cheers,
> Szilárd
>
>
>>
>>
>> James
>>
>>
>> 2013/1/21 Szilárd Páll :
>> > Szilárd
>> --
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Re: [gmx-users] Getting the virial for each individual atom.

[Timothy Sirk]

Zach,

If you aren't using PBC, then how about saving total forces per atom and
use 'ri outer Fi' for the per-atom virial? And, if you want it, get the
kinetic part from 'm* (vi outer vi)'.

The virial shouldn't have to come from ij pairs, although that is certainly
a good way to get it.

Tim

On Tue, Jan 22, 2013 at 11:05 AM, Marcin, Zachary  wrote:

> Tim,
> The PBC's were turned off and need to be for what we're trying to do.
> Pretty much everything that might work, as far as I've seen, can't unless
> we change some source code to do what we need.
> Thanks,
> Zach
>
> On Mon, Jan 21, 2013 at 4:47 PM, Timothy Sirk  wrote:
>
> > Zach,
> >
> > Do you have periodic system with charges? For PBC, you might try one of
> the
> > forms in J. Chem. Phys. 131 154107 (2009). Electrostatics are more
> work...
> > For Ewald sum and PPPM contribution, you could check refs in
> > lammps.sandia.gov/doc/PDF/kspace.pdf
> >
> > We have an upcoming paper that explains in more detail how to do this
> with
> > PPPM and gives an example with heat flux. Maybe something similar could
> be
> > done in GROMACS with PME.
> >
> > best,
> >
> > Tim
> >
> >
> > On Mon, Jan 21, 2013 at 1:06 PM, Marcin, Zachary
> > wrote:
> >
> > > Berk,
> > > Here is where I think I might be able to:
> > > In calcvir.c there is a method called calc_vir which takes, among other
> > > things, int nxf(no idea what this does), rvec x[], and revec f[].  It
> > then
> > > does dvxx+= x[i][xx] *f[i][XX];.
> > > This is the same as the formula that I am trying to solve for (Vi*Pi +
> > > .5*SUM(Rij * Fij)).
> > > What I figured I could do is create another array to calculate the
> > virials
> > > for, thus giving me an index position per atom, and then use that
> > somehow.
> > >
> > > I also know that I can use R(ij) * F(ij), or the distance between
> atoms i
> > > and j times the Forces between atoms i and j.  If anyone has any
> insight
> > on
> > > getting these, that could also work.
> > > I know how to get the individual positions, but I don't know how I
> would
> > go
> > > about the forces aspect of that.
> > >
> > > Thanks,
> > > Zach
> > >
> > > On Mon, Jan 21, 2013 at 12:44 PM, Berk Hess  wrote:
> > >
> > > >
> > > > Hi,
> > > >
> > > > The virial has no meaning per atom.
> > > > And you can't get the virial per atom out of Gromacs, it is never
> > > > calculated in that way (see the manual for details).
> > > > A special local pressure version of Gromacs exists, but even there
> you
> > > > won't get a virial per atom.
> > > >
> > > > Cheers,
> > > >
> > > > Berk
> > > >
> > > > 
> > > > > Date: Mon, 21 Jan 2013 12:35:04 -0500
> > > > > From: zachary.mar...@wilkes.edu
> > > > > To: gmx-users@gromacs.org
> > > > > Subject: [gmx-users] Getting the virial for each individual atom.
> > > > >
> > > > > Hello,
> > > > > For the research I'm working with, I need to get the virial for
> each
> > > > > individual atom in the system. I've been tracing all of the calls
> > made
> > > in
> > > > > the methods related to virials(Version 4.5.5) and this is the call
> > > stack
> > > > > that I think has what I need.
> > > > > mdrun.c -> do_md in md.c -> do_force in sim_util.c -> calcvir.c
> > > > >
> > > > > I have a few questions that I was wondering if anyone could answer.
> > > > >
> > > > > 1. In sim_util.c, there is a comment that says "Total virial
> computed
> > > in
> > > > > global_stat, called from do_md". I cannot find where this is called
> > in
> > > > > do_md. Was this changed at any point and the comment was still left
> > in
> > > > the
> > > > > code?
> > > > >
> > > > > 2. If I change the codes in calcvir.c to find the virials for each
> > > > > individual atom, say by piping the atom numbers and forces and
> > > everything
> > > > > needed into another program so it doesn't effect the way that
> gromacs
> > > > runs
> > > > > and will still allow everything to do what it needs, will this be
> > > screwed
> > > > > up by/screw up the domain decomposition/the mpi stuff?
> > > > >
> > > > > Basically, I'm looking for advice on a method to output the
> > individual
> > > > > virials for each atom for each frame, instead of just the final
> > output
> > > of
> > > > > the average virial on the entire system.
> > > > > Thanks,
> > > > > Zach Marcin
> > > > > Wilkes University
> > > > > --
> > > > > gmx-users mailing list gmx-users@gromacs.org
> > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > > > * Pl

Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian

[Szilárd Páll]

On Tue, Jan 22, 2013 at 12:45 PM, James Starlight wrote:

> Szilárd,
>
> Today I've tried to re-install cuda+gromacs and do apt-get
> distr-upgrade but the same error was obtained during gromacs
>

I'm don't see how does the distribution upgrade relate to the issues you
had (except if you have updated glibs to a newer version which is *still*
incompatible with libcuda. You should probably try getting a more recent
glibc and GCC version, one that libcuda is linked against. However, I'm not
sure what the source of your problem is, so I can't suggest a certain
solution.

> compilation. By the way where I could provide --add-needed option ?

CMAKE_EXE_LINKER_FLAGS=-wl,--add-needed

Cheers,
Szilárd


>
>
> James
>
>
> 2013/1/21 Szilárd Páll :
> > Szilárd
> --
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Re: [gmx-users] clusterization in dihedral space

[Justin Lemkul]

On 1/22/13 1:17 PM, francesco oteri wrote:

Thank you Mark and Justin,
do you have any reference where this kind of clustering is explained?



What clustering?  I assumed that you had a definition of what you wanted to 
define when you posed the original question.



I mean, since i need a parameter representing the difference between two
frames
to build the matrix, what is the parameter I can use starting from the
dihedrals?



Perhaps you should find a literature example of what you want to do and revisit 
Chapter 8 of the manual, then pose a more direct question.  In order to provide 
you an answer to this question, we need to know (1) what you've done, (2) what 
you're thinking of doing, and (3) what you're actually measuring.  Since we know 
none of these, it's impossible to give any sort of recommendation.


-Justin

--


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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] clusterization in dihedral space

[francesco oteri]

Thank you Mark and Justin,
do you have any reference where this kind of clustering is explained?

I mean, since i need a parameter representing the difference between two
frames
to build the matrix, what is the parameter I can use starting from the
dihedrals?

Francesco



2013/1/22 Mark Abraham 

> On Mon, Jan 21, 2013 at 8:06 PM, francesco oteri
> wrote:
>
> > Thank you,
> > but I don't see how performing cluster analysis with g_angle
> >
>
> g_dih never did do any clustering. As Justin said, g_angle with a suitable
> index group likely does the job for you.
>
> Mark
> --
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-- 
Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] clusterization in dihedral space

[Mark Abraham]

On Mon, Jan 21, 2013 at 8:06 PM, francesco oteri
wrote:

> Thank you,
> but I don't see how performing cluster analysis with g_angle
>

g_dih never did do any clustering. As Justin said, g_angle with a suitable
index group likely does the job for you.

Mark
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Re: [gmx-users] Re: Temperature coupling problem: reference T is different to given T in mdp file

[Mark Abraham]

On Tue, Jan 22, 2013 at 4:56 PM, Andrey Frolov wrote:

>
> 3) However, it is still not clear to me why for the wrong coulombtype setup
> :
> - Nose-Hoover with 1 chain + leap-frog ("md") integrator gives desired
> average T,
> - Nose-Hoover with 1 or 10 chain(s) + velocity Verlet ("md-vv") integrator
> does NOT give desired average T ?
>

Unfortunately, md-vv has not been very well tested in a range of
integration contexts (e.g. in 4.5.5 and earlier it is broken with v-rescale
thermostat). If you have a .tpr that shows problems with 4.5.5 or 4.6, then
we want to have a look at it urgently. Please file an issue here
http://redmine.gromacs.org/ and attach a .tpr for us (preferably with a
sound electrostatics setup, but if you only get the problem with the
unsound setup, that may illustrate a real problem for us).

Mark
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Re: [gmx-users] Getting the virial for each individual atom.

[Marcin, Zachary]

Tim,
The PBC's were turned off and need to be for what we're trying to do.
Pretty much everything that might work, as far as I've seen, can't unless
we change some source code to do what we need.
Thanks,
Zach

On Mon, Jan 21, 2013 at 4:47 PM, Timothy Sirk  wrote:

> Zach,
>
> Do you have periodic system with charges? For PBC, you might try one of the
> forms in J. Chem. Phys. 131 154107 (2009). Electrostatics are more work...
> For Ewald sum and PPPM contribution, you could check refs in
> lammps.sandia.gov/doc/PDF/kspace.pdf
>
> We have an upcoming paper that explains in more detail how to do this with
> PPPM and gives an example with heat flux. Maybe something similar could be
> done in GROMACS with PME.
>
> best,
>
> Tim
>
>
> On Mon, Jan 21, 2013 at 1:06 PM, Marcin, Zachary
> wrote:
>
> > Berk,
> > Here is where I think I might be able to:
> > In calcvir.c there is a method called calc_vir which takes, among other
> > things, int nxf(no idea what this does), rvec x[], and revec f[].  It
> then
> > does dvxx+= x[i][xx] *f[i][XX];.
> > This is the same as the formula that I am trying to solve for (Vi*Pi +
> > .5*SUM(Rij * Fij)).
> > What I figured I could do is create another array to calculate the
> virials
> > for, thus giving me an index position per atom, and then use that
> somehow.
> >
> > I also know that I can use R(ij) * F(ij), or the distance between atoms i
> > and j times the Forces between atoms i and j.  If anyone has any insight
> on
> > getting these, that could also work.
> > I know how to get the individual positions, but I don't know how I would
> go
> > about the forces aspect of that.
> >
> > Thanks,
> > Zach
> >
> > On Mon, Jan 21, 2013 at 12:44 PM, Berk Hess  wrote:
> >
> > >
> > > Hi,
> > >
> > > The virial has no meaning per atom.
> > > And you can't get the virial per atom out of Gromacs, it is never
> > > calculated in that way (see the manual for details).
> > > A special local pressure version of Gromacs exists, but even there you
> > > won't get a virial per atom.
> > >
> > > Cheers,
> > >
> > > Berk
> > >
> > > 
> > > > Date: Mon, 21 Jan 2013 12:35:04 -0500
> > > > From: zachary.mar...@wilkes.edu
> > > > To: gmx-users@gromacs.org
> > > > Subject: [gmx-users] Getting the virial for each individual atom.
> > > >
> > > > Hello,
> > > > For the research I'm working with, I need to get the virial for each
> > > > individual atom in the system. I've been tracing all of the calls
> made
> > in
> > > > the methods related to virials(Version 4.5.5) and this is the call
> > stack
> > > > that I think has what I need.
> > > > mdrun.c -> do_md in md.c -> do_force in sim_util.c -> calcvir.c
> > > >
> > > > I have a few questions that I was wondering if anyone could answer.
> > > >
> > > > 1. In sim_util.c, there is a comment that says "Total virial computed
> > in
> > > > global_stat, called from do_md". I cannot find where this is called
> in
> > > > do_md. Was this changed at any point and the comment was still left
> in
> > > the
> > > > code?
> > > >
> > > > 2. If I change the codes in calcvir.c to find the virials for each
> > > > individual atom, say by piping the atom numbers and forces and
> > everything
> > > > needed into another program so it doesn't effect the way that gromacs
> > > runs
> > > > and will still allow everything to do what it needs, will this be
> > screwed
> > > > up by/screw up the domain decomposition/the mpi stuff?
> > > >
> > > > Basically, I'm looking for advice on a method to output the
> individual
> > > > virials for each atom for each frame, instead of just the final
> output
> > of
> > > > the average virial on the entire system.
> > > > Thanks,
> > > > Zach Marcin
> > > > Wilkes University
> > > > --
> > > > 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!
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> > > > www interface or send it to gmx-users-requ...@gromacs.org.
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> > >   --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > >
> > --
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> > www interface or

[gmx-users] Re: Temperature coupling problem: reference T is different to given T in mdp file

[Andrey Frolov]

1) I am very sorry, i misled you in the previous post. It turned out that by
mistake (stupid!) for my umbrella simulations i used "coulombtype = Cut-off" 
instead of "coulombtype = PME". 

2) *The problem resolved* :). The "coulombtype = Cut-off" in combination
with "rlist = rcoulomb"  and "nstlist > 1" produces the wrong average
temperature, due to poor energy conservation and heating of the system in
between subsequent temperature updates by v-rescale thermostat.

3) However, it is still not clear to me why for the wrong coulombtype setup
:
- Nose-Hoover with 1 chain + leap-frog ("md") integrator gives desired
average T, 
- Nose-Hoover with 1 or 10 chain(s) + velocity Verlet ("md-vv") integrator
does NOT give desired average T ? 

Justin, thank you very much for pointing me to the Cut-off issue and other
suggestions. 

Andrey




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Re: [gmx-users] calculate area per lipid and bilayer thickness versus time

[Kieu Thu Nguyen]

Thank Justin so much ! Sorry about my stupid question. I have looked the
algorithm and i got it.


On Tue, Jan 22, 2013 at 8:05 PM, Justin Lemkul  wrote:

>
>
> On 1/22/13 12:00 AM, Kieu Thu Nguyen wrote:
>
>> Thank Justin ! And i used GridMAT-MD as you advised.
>>
>> I got result "The average bilayer "thickness" will be printed to
>> 50x50_average_pbc.dat". But that result is only equal to a half of
>> experiment result. I think "bilayer thickness" is equal to the sum of "top
>> leaflet thickness" and "bottom leaflet thickness". So should i double "The
>> average bilayer "thickness"..." mentioned above ?
>>
>>
> No.  The program measures the total thickness, using the reference atoms
> you provide.  The individual files ("top thickness" and "bottom thickness")
> represent two ways of measuring the same thing, using both leaflets as
> reference, which are then averaged to produce the desired distance file.
>  Please refer to our paper for the algorithm.
>
>
>  And i do not get average area per lipd, just "The average area per lipid
>> in
>> the top leaflet is 64.2329395973154 sq. Angstroms. The average area per
>> lipid in the bottom leaflet is 63.3821721854305 sq. Angstroms".
>>
>>
> The data file contains areas for each individual lipid, which can be
> averaged.
>
> -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] 2 amino_acid outside the box before animation in ngmx

[Justin Lemkul]

On 1/22/13 9:35 AM, Devika N T wrote:

Dear all

I have performed 1ns simulation for my protein (148 aa) complexed with calcium
ion.
After the generation of 1ns files, I have given *"ngmx"* to view the protein
.
But I can see 2 amino acids residues out of the box before giving the
"animation" option in "ngmx"

While giving the "animation"  option at around 980ps th 2 residues are
going inside the box.

Box shape given : octahedron with "2" and centered.

What could be the reason..


http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-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] Re: Temperature coupling problem: reference T is different to given T in mdp file

[Justin Lemkul]

On 1/22/13 9:27 AM, Andrey Frolov wrote:

Dear Justin,


Considering all data points will include early frames that are not
necessarily
anywhere close to being equilibrated.  You could try block averaging to see

if

the results converge to the correct result over the latter part of the
simulation, or at least see if the system is approaching the target

temperature.

Temperature jumps to the "wrong" target temperature at the beginning of the
simulation (see the figure attached). So, this is not the reason of the
problem.





It would be better to diagnose the system using PME.  Even if the results
are
"similar," rounding errors are compounded when using plain cutoffs, which
render
the results inherently unreliable.


This is true. But, the problem persists even with PME. I have simulations
with slightly different setup: more CO2 molecules and higher CO2
concentration, umbrella windows for different separations between
paracetamol molecules, 24 ns simulation time, with PME electrostatics. Here
it gives me the "wrong" average temperature 478.486 K, while i set v-rescale
thermostat to 423.15 K. So, electrostatics method seems to play no role in
this.


Moreover, i tested the same simulation setups as in the initial posts with
Nose-Hoover thermostat. Single Nose-Hoover with number of chains = 1 gives
correct temperatures (the same as a set in mdp file). Even if i set three
thermostats to three subsystems (eventhough, i agree that this approach is
valid only for testing purposes) the resulting temperatures are correct.

But with N chains = 10, the resulting temperatures are again wrong (up to ~
20 K). (In this case integrator was md-vv).



As additional tests, can you set dt = 0.001 with the current setup, and then 
also try constraining all bonds rather than just hbonds (with dt = 0.002)?


-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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[gmx-users] Re: Temperature coupling problem: reference T is, different to given T in mdp file

[Thomas Schlesier]

Hi,
you use a relative high tau_t:
>> >tcoupl = v-rescale
>> >tc-grps = CO2 PARA PAR2
>> >tau_t = 1.0 1.0 1.0
>> >ref_t = 410 410 410
In my simulations i use a value of 0.1
don't know if this would help, but it was the only thing which catched 
my eye, as i read you .mdp parameters.


Greetings
Thomas



Am 22.01.2013 15:36, schrieb gmx-users-requ...@gromacs.org:

   Dear gmx-users,
>
>1) I am running simulation of two paracetamol molecules dissolved in 
supercritical CO2 in NVT ensemble.  The problem is that the resulting temperature 
of the system is larger than the temperature specified in mdp file by ~ 20 K (i 
set ref_t = 410 K in mdp file).  Berendsen and v-rescale thermostats  behave 
similarly. The output from g_energy:
>"
>Statistics over 250001 steps [ 0. through 500. ps ], 1 data sets
>All statistics are over 2501 points
>Energy Average Err.Est. RMSD Tot-Drift
>---
>T-System 430.3421.1 14.1796 6.30923 (K)
>"
>
>
>2) When i run the same simulation but set 3 different subsystems (all CO2 
molecules, the first paracetamol molecule, the second paracetamol molecule)  
coupled to different bathes with the same temperature, the resulting temperatures 
do not match the specified temperature = 410 K. The output from g_energy:
>"

This approach is unsound.  There are insufficient degrees of freedom in single
molecules to justify distinct thermostats.


>Statistics over 250001 steps [ 0. through 500. ps ], 4 data sets
>All statistics are over 2501 points
>Energy Average Err.Est. RMSD Tot-Drift
>---
>Temperature428.821.2 14.356 -3.39055 (K)
>T-CO2  427.432  1.2 14.6848 -5.24 (K)
>T-PARA452.434  3.7 91.2873 20.656 (K)
>T-PAR2454.211  10  93.7436 37.8375 (K) "
>
>I would appreciate very much if someone gives me a hint what could be wrong.

Considering all data points will include early frames that are not necessarily
anywhere close to being equilibrated.  You could try block averaging to see if
the results converge to the correct result over the latter part of the
simulation, or at least see if the system is approaching the target temperature.


>Some information about system:
>There are 200 CO2 molecules, cubic box: 4 x 4 x 4 nm3. I set "coulombtype = 
Cut-off" just for testing purposes, PME gives similar results.
>

It would be better to diagnose the system using PME.  Even if the results are
"similar," rounding errors are compounded when using plain cutoffs, which render
the results inherently unreliable.

-Justin


>Some mdp control options (for the 2) case):
>"
>; RUN CONTROL PARAMETERS =
>integrator = md
>dt = 0.002
>nsteps = 25
>comm-mode = Linear
>nstcomm = 1
>; NEIGHBORSEARCHING PARAMETERS =
>nstlist = 10
>ns_type = grid
>pbc = xyz
>rlist = 1.1
>; OPTIONS FOR ELECTROSTATICS AND VDW =
>coulombtype = Cut-off
>rcoulomb = 1.1
>vdw_type = Shift
>rvdw = 1.0
>; OPTIONS FOR WEAK COUPLING ALGORITHMS =
>tcoupl = v-rescale
>tc-grps = CO2 PARA PAR2
>tau_t = 1.0 1.0 1.0
>ref_t = 410 410 410
>; GENERATE VELOCITIES FOR STARTUP RUN =
>gen_vel = yes
>gen_temp = 410
>gen_seed = 473529
>; OPTIONS FOR BONDS =
>constraints = hbonds
>constraint_algorithm = lincs
>unconstrained_start = no
>shake_tol = 0.1
>lincs_order = 4
>lincs_warnangle = 30
>morse = no
>lincs_iter = 2 "


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[gmx-users] Re: Temperature coupling problem: reference T is different to given T in mdp file

[Andrey Frolov]

Dear Justin,

> Considering all data points will include early frames that are not
> necessarily 
>anywhere close to being equilibrated.  You could try block averaging to see
if 
>the results converge to the correct result over the latter part of the 
>simulation, or at least see if the system is approaching the target
temperature.

Temperature jumps to the "wrong" target temperature at the beginning of the
simulation (see the figure attached). So, this is not the reason of the
problem. 


 


> It would be better to diagnose the system using PME.  Even if the results
> are 
> "similar," rounding errors are compounded when using plain cutoffs, which
> render 
> the results inherently unreliable.

This is true. But, the problem persists even with PME. I have simulations
with slightly different setup: more CO2 molecules and higher CO2
concentration, umbrella windows for different separations between
paracetamol molecules, 24 ns simulation time, with PME electrostatics. Here
it gives me the "wrong" average temperature 478.486 K, while i set v-rescale
thermostat to 423.15 K. So, electrostatics method seems to play no role in
this. 


Moreover, i tested the same simulation setups as in the initial posts with
Nose-Hoover thermostat. Single Nose-Hoover with number of chains = 1 gives
correct temperatures (the same as a set in mdp file). Even if i set three
thermostats to three subsystems (eventhough, i agree that this approach is
valid only for testing purposes) the resulting temperatures are correct.

But with N chains = 10, the resulting temperatures are again wrong (up to ~
20 K). (In this case integrator was md-vv).

Andrey






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Re: [gmx-users] Temperature coupling problem: reference T is different to given T in mdp file

[Justin Lemkul]

On 1/22/13 4:58 AM, Andrey Frolov wrote:

  Dear gmx-users,

1) I am running simulation of two paracetamol molecules dissolved in 
supercritical CO2 in NVT ensemble.  The problem is that the resulting 
temperature of the system is larger than the temperature specified in mdp file 
by ~ 20 K (i set ref_t = 410 K in mdp file).  Berendsen and v-rescale 
thermostats  behave similarly. The output from g_energy:
"
Statistics over 250001 steps [ 0. through 500. ps ], 1 data sets
All statistics are over 2501 points
Energy Average Err.Est. RMSD Tot-Drift
---
T-System 430.3421.1 14.1796 6.30923 (K)
"


2) When i run the same simulation but set 3 different subsystems (all CO2 
molecules, the first paracetamol molecule, the second paracetamol molecule)  
coupled to different bathes with the same temperature, the resulting 
temperatures do not match the specified temperature = 410 K. The output from 
g_energy:
"


This approach is unsound.  There are insufficient degrees of freedom in single 
molecules to justify distinct thermostats.



Statistics over 250001 steps [ 0. through 500. ps ], 4 data sets
All statistics are over 2501 points
Energy Average Err.Est. RMSD Tot-Drift
---
Temperature428.821.2 14.356 -3.39055 (K)
T-CO2  427.432  1.2 14.6848 -5.24 (K)
T-PARA452.434  3.7 91.2873 20.656 (K)
T-PAR2454.211  10  93.7436 37.8375 (K) "

I would appreciate very much if someone gives me a hint what could be wrong.


Considering all data points will include early frames that are not necessarily 
anywhere close to being equilibrated.  You could try block averaging to see if 
the results converge to the correct result over the latter part of the 
simulation, or at least see if the system is approaching the target temperature.



Some information about system:
There are 200 CO2 molecules, cubic box: 4 x 4 x 4 nm3. I set "coulombtype = 
Cut-off" just for testing purposes, PME gives similar results.



It would be better to diagnose the system using PME.  Even if the results are 
"similar," rounding errors are compounded when using plain cutoffs, which render 
the results inherently unreliable.


-Justin


Some mdp control options (for the 2) case):
"
; RUN CONTROL PARAMETERS =
integrator = md
dt = 0.002
nsteps = 25
comm-mode = Linear
nstcomm = 1
; NEIGHBORSEARCHING PARAMETERS =
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.1
; OPTIONS FOR ELECTROSTATICS AND VDW =
coulombtype = Cut-off
rcoulomb = 1.1
vdw_type = Shift
rvdw = 1.0
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
tcoupl = v-rescale
tc-grps = CO2 PARA PAR2
tau_t = 1.0 1.0 1.0
ref_t = 410 410 410
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = yes
gen_temp = 410
gen_seed = 473529
; OPTIONS FOR BONDS =
constraints = hbonds
constraint_algorithm = lincs
unconstrained_start = no
shake_tol = 0.1
lincs_order = 4
lincs_warnangle = 30
morse = no
lincs_iter = 2 "


















--


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] calculate area per lipid and bilayer thickness versus time

[Justin Lemkul]

On 1/22/13 12:00 AM, Kieu Thu Nguyen wrote:

Thank Justin ! And i used GridMAT-MD as you advised.

I got result "The average bilayer "thickness" will be printed to
50x50_average_pbc.dat". But that result is only equal to a half of
experiment result. I think "bilayer thickness" is equal to the sum of "top
leaflet thickness" and "bottom leaflet thickness". So should i double "The
average bilayer "thickness"..." mentioned above ?



No.  The program measures the total thickness, using the reference atoms you 
provide.  The individual files ("top thickness" and "bottom thickness") 
represent two ways of measuring the same thing, using both leaflets as 
reference, which are then averaged to produce the desired distance file.  Please 
refer to our paper for the algorithm.



And i do not get average area per lipd, just "The average area per lipid in
the top leaflet is 64.2329395973154 sq. Angstroms. The average area per
lipid in the bottom leaflet is 63.3821721854305 sq. Angstroms".



The data file contains areas for each individual lipid, which can be averaged.

-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] Problem with gromacs-4.6 compilation on Debian

[James Starlight]

Szilárd,

Today I've tried to re-install cuda+gromacs and do apt-get
distr-upgrade but the same error was obtained during gromacs
compilation. By the way where I could provide --add-needed option ?


James


2013/1/21 Szilárd Páll :
> Szilárd
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[gmx-users] 27th Molecular Modelling Workshop 2013 Feb., 25th-27th in Erlangen, Germany

[Harald Lanig]

Dear Colleagues,
I would like to bring to your attention that the 27th Molecular
Modeling Workshop will be taking place in Erlangen from February 25th
to 27th 2013.

The goal of the Workshop is to give young scientists, especially PhD
students and Post-Docs, the chance to present their current research,
and colleagues from the industry will be able to gain an overview about
current academic research.

Contributions from all areas of molecular modelling, life sciences to
materials are highly welcome!

We are pleased to announce that the following scientists (in
alphabetical order) have agreed to give plenary lectures:

Prof. Jamshed Anwar (Lancaster University)
"Developing simple physics-type force field models for molecular simulation"

Dr. Hans Matter (Sanofi)
"Interactions of Halogen Atoms to Protein Binding Sites and 
Contributions to Binding Affinity"


Prof. Carsten Schmuck (University Duisburg-Essen)
"Quantifying noncovalent interactions using artifical receptors as model 
systems"


Prof. Susan B. Sinnott (University of Florida)
"Next Generation Classical Potentials for Modeling Many-Body 
Interactions in Materials"


For any further information regarding the program, registration,
location, and accommodation, please refer to the following website:
http://mmws2013.mgms-ds.de/

The deadline for registration is 25th January 2013.

Best regards
Stefan Guessregen
Harald Lanig

--

 PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen

 Phone +49(0)9131-85 26525   harald DOT lanig AT chemie.uni-erlangen.de
 Fax   +49(0)9131-85 26565   http://www.chemie.uni-erlangen.de/lanig

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[gmx-users] Re: Temperature coupling problem: reference T is different to given T in mdp file

[Andrey Frolov]

I am sorry, forgot to add: i use gromacs-4.6 at the moment. For gromacs-4.5.4 
there is the same problem



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[gmx-users] Temperature coupling problem: reference T is different to given T in mdp file

[Andrey Frolov]

 Dear gmx-users,

1) I am running simulation of two paracetamol molecules dissolved in 
supercritical CO2 in NVT ensemble.  The problem is that the resulting 
temperature of the system is larger than the temperature specified in mdp file 
by ~ 20 K (i set ref_t = 410 K in mdp file).  Berendsen and v-rescale 
thermostats  behave similarly. The output from g_energy:
"
Statistics over 250001 steps [ 0. through 500. ps ], 1 data sets
All statistics are over 2501 points
Energy Average Err.Est. RMSD Tot-Drift
---
T-System     430.342    1.1 14.1796 6.30923 (K)
"


2) When i run the same simulation but set 3 different subsystems (all CO2 
molecules, the first paracetamol molecule, the second paracetamol molecule)  
coupled to different bathes with the same temperature, the resulting 
temperatures do not match the specified temperature = 410 K. The output from 
g_energy: 
"
Statistics over 250001 steps [ 0. through 500. ps ], 4 data sets
All statistics are over 2501 points
Energy Average Err.Est. RMSD Tot-Drift
---
Temperature    428.82            1.2     14.356 -3.39055 (K)
T-CO2              427.432          1.2     14.6848 -5.24 (K)
T-PARA            452.434          3.7     91.2873 20.656 (K)
T-PAR2            454.211          10      93.7436 37.8375 (K) "

I would appreciate very much if someone gives me a hint what could be wrong.
Thank you.

Andrey

Andrey I. Frolov, PhD
Postdoctoral fellow
Institute of Solution Chemistry
Russian Academy of Sciences


Some information about system:
There are 200 CO2 molecules, cubic box: 4 x 4 x 4 nm3. I set "coulombtype = 
Cut-off" just for testing purposes, PME gives similar results. 

Some mdp control options (for the 2) case):
"
; RUN CONTROL PARAMETERS = 
integrator = md
dt = 0.002
nsteps = 25
comm-mode = Linear
nstcomm = 1
; NEIGHBORSEARCHING PARAMETERS = 
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.1
; OPTIONS FOR ELECTROSTATICS AND VDW = 
coulombtype = Cut-off
rcoulomb = 1.1
vdw_type = Shift 
rvdw = 1.0
; OPTIONS FOR WEAK COUPLING ALGORITHMS = 
tcoupl = v-rescale
tc-grps = CO2 PARA PAR2
tau_t = 1.0 1.0 1.0
ref_t = 410 410 410
; GENERATE VELOCITIES FOR STARTUP RUN = 
gen_vel = yes
gen_temp = 410 
gen_seed = 473529
; OPTIONS FOR BONDS = 
constraints = hbonds
constraint_algorithm = lincs
unconstrained_start = no
shake_tol = 0.1
lincs_order = 4
lincs_warnangle = 30
morse = no
lincs_iter = 2 "














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