[gmx-users] Fwd: Question about editconf -noc flag

[James Lord]

Hi all,
I have made an oil slab (energy minimized, equilibrated nvt and npt), some
of the oil molecules are at the other end (periodicity).
https://drive.google.com/open?id=0B0YMTXH1gmQsYmdvQ3huYWtDaGs

then I decided to increase the box size in z direction a bit to make enough
room for protein, using

editconf -f OCT_npt.gro -oOCT_newbox.gro -box  6.47271 6.47271 16 -noc

https://drive.google.com/open?id=0B0YMTXH1gmQsT1M3dzBNNTJrT28

I used the last flag to put the oil at the ends of box but it is not doing
for one end? any thoughts?
Cheers
James
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[gmx-users] Question about editconf -noc flag

[James Lord]

Hi all,
I have made an oil slab (energy minimized, equilibrated nvt and npt), some
of the oil molecules are at the other end (periodicity).
https://drive.google.com/open?id=0B0YMTXH1gmQsYmdvQ3huYWtDaGs

then I decided to increase the box size in z direction a bit to make enough
room for protein, using

editconf -f OCT_npt.gro -oOCT_newbox.gro -box  6.47271 6.47271 16 -noc

https://drive.google.com/file/d/0B0YMTXH1gmQsYmdvQ3huYWtDaGs/view?usp=sharing
I used the last flag to put the oil at the ends of box but it is not doing
for one end? any thoughts?
Cheers
James
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Re: [gmx-users] Atom type SDMSO not found

[Sun Iba]

Here is the generated topology of ligand with PRODRG server, i believe
something is wrong with atom typs here;

 PRODRG COORDS
   29
1UNK  CLAW 1   1.328  -0.638  -0.151
1UNK  CAM  2   1.384  -0.765  -0.049
1UNK  SAU  3   1.520  -0.861  -0.089
1UNK  CAG  4   1.503  -0.954   0.053
1UNK  CLAV 5   1.606  -1.085   0.095
1UNK  CAN  6   1.396  -0.913   0.128
1UNK  HAR  7   1.368  -0.958   0.223
1UNK  CAO  8   1.327  -0.803   0.069
1UNK  SAT  9   1.181  -0.728   0.145
1UNK  OAR 10   1.144  -0.805   0.261
1UNK  OAS 11   1.215  -0.589   0.171
1UNK  NAQ 12   1.058  -0.732   0.029
1UNK  HAS 13   1.052  -0.655  -0.035
1UNK  CAC 14   0.963  -0.835   0.018
1UNK  CAD 15   0.837  -0.802  -0.035
1UNK  HAD 16   0.817  -0.699  -0.065
1UNK  CAE 17   0.739  -0.899  -0.051
1UNK  HAE 18   0.642  -0.870  -0.093
1UNK  CAB 19   0.987  -0.969   0.051
1UNK  HAB 20   1.085  -0.998   0.090
1UNK  CAA 21   0.887  -1.065   0.036
1UNK  HAA 22   0.908  -1.168   0.066
1UNK  CAF 23   0.759  -1.034  -0.015
1UNK  NAP 24   0.657  -1.133  -0.031
1UNK  CAH 25   0.519  -1.090  -0.064
1UNK  CAI 26   0.421  -1.196  -0.011
1UNK  CAJ 27   0.447  -1.336  -0.069
1UNK  CAK 28   0.595  -1.359  -0.104
1UNK  CAL 29   0.690  -1.276  -0.016
   1.33540   1.33540   1.33540

The atom types look strange to me. Please help

On Wed, Jul 29, 2015 at 10:18 AM, su  wrote:

> Hello everyone
> I am doing protein-ligand simulation according to Justin's tutorial. After
> running gmx grompp command, i encountered following error:
> Fatal error:
> Atomtype SDMSO not found.
> Is this the force field matching problem? because i am not able to find
> out any such atom types in any of the generated files.
> Please guide me where the problem is. All other commands ran properly.
>
> Suniba
> Sent from my iPhone
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[gmx-users] Atom type SDMSO not found

[su]

Hello everyone
I am doing protein-ligand simulation according to Justin's tutorial. After 
running gmx grompp command, i encountered following error: 
Fatal error: 
Atomtype SDMSO not found.
Is this the force field matching problem? because i am not able to find out any 
such atom types in any of the generated files. 
Please guide me where the problem is. All other commands ran properly. 

Suniba
Sent from my iPhone
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Re: [gmx-users] Question about forcefield files

[Michael Shirts]

The identifiers are just strings, so as long as they are unique, there
shouldn't be a problem (I can't remember offhand if capitalization is
respected or not, though).

I'd name them something other than opls_XXX, though, if you are adding
your own, just to avoid confusion of you share the files with others.

On Tue, Jul 28, 2015 at 3:43 PM, Eric Smoll  wrote:
> Hello GROMACS users,
>
> In the OPLS atomtypes.atp file, is it problematic to define atom type names
> (e.g., "opls_XXX") with nonconsecutive integers? For example,
>
> opls_1000 ...
> opls_1100 ...
> opls_1050 ...
>
> Best,
> Eric
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[gmx-users] Question about forcefield files

[Eric Smoll]

Hello GROMACS users,

In the OPLS atomtypes.atp file, is it problematic to define atom type names
(e.g., "opls_XXX") with nonconsecutive integers? For example,

opls_1000 ...
opls_1100 ...
opls_1050 ...

Best,
Eric
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Re: [gmx-users] Measuring Bilayer thickness with gmx distance in CGMD simulations

[Carlos Navarro Retamal]

Hi Teemu,
Thanks for the reply.
Unfortunately, i cannot upgrade to 5.0.6 right now ( i have to ask to the admin 
of the cluster first, and so on and so far).
I do can downgrade to 4.6.3 and use g_dist instead.
I have read some papers where people claimed to have been used g_dist to 
measure the thickness of a bilayer, but I wasn’t capable to do that.
I created 3 different groups:
All PO4 beads of the bilayer: G1
PO4 beads of the top leaflet of the bilayer: G2
PO4 beads of the bottom leaflet of the bilayer: G3
but considering that g_dist used the COM of the groups when i used g_dist as 
following:
g_dist -f POPC-300K-2us.xtc -s POPC-300K-2us.tpr -n index.ndx -o PO4-distance

If i select group 1 and 2 as group G1 i got a distance of 0 (which i think it 
make sense, considering that g_dist use the COM of a group)
but when i select group 1: G2 and group 2: G3 (PO4 beads of the top  and bottom 
leaflet respectively) i got really nice values:
~3.9 at 300K
~3.8 at 328K
with an standard deviation of ~0.002 each (considering the Z component, of 
course)
Are this results ok? Can i use this approximation  (measuring the distance 
between the top and bottom PO4 beads of a bilayer) to get the membrane 
thickness of a bilayer?
Best,
Carlos
--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarr...@gmail.com or cnava...@utalca.cl



On July 28, 2015 at 3:17:47 PM, Teemu Murtola 
(teemu.murt...@gmail.com) wrote:

Please upgrade to 5.0.6. There was a bug with gmx distance -oxyz that
caused the output file to not appear (or to overwrite some unintended
files), which was fixed for the latest version.

On Tue, Jul 28, 2015, 17:34 Carlos Navarro Retamal 
wrote:

> Hi Justin,
> thanks for your reply.
> Is there a way, to analyse each component (x,y,z) of the distance without
> the flag -oxyz?
> For some reason, I’m unable to get this data with gmx distance.
> In fact, when i ran
> gmx distance -f trajout329K.xtc -s POPC-329K-2us.tpr -n index.ndx -oxyz
> the command line doesn’t generate anything (any *xvg file).
> I don’t know what I’m doing wrong
> Best,
> Carlos
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
>
>
> On July 28, 2015 at 9:34:32 AM, Justin Lemkul (jalem...@vt.edu jalem...@vt.edu>) wrote:
>
> July 28, 2015 at 6:09:51 AM GMT-3 ro Retamal wrote:
> > Dear gmx users,
> > I’m studying the implication of higher temperatures in the membrane
> thickness (d) of several bilayer during CGMD simulations.
> > In order to measure d in a pure POPC membrane i create an index group
> containing only PO4 beads.
> > Before everything, i remove PBC conditions in the simulations as
> following:
> > trjconv -f POPC-300K-2us.xtc -s POPC-300K-2us.tpr -pbc nojump -o
> trajout300K.xtc
> > trjconv -f POPC-329K-2us.xtc -s POPC-329K-2us.tpr -pbc nojump -o
> trajout329K.xtc
> >
> > Then, I used gmx distance:
> > gmx distance -f trajout300K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav
> avg-300K
> > gmx distance -f trajout329K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav
> avg-329K
> >
> > Finally, using g_analyse i analyse both *xvg files and i got:
> >
> > 300K:
> > Average distance: 4.090 nm
> > Standard deviation: 1.451 nm
> >
> > 329K:
> > Average distance: 4.134 nm
> > Standard deviation: 1.515 nm
> >
>
> Those are pretty massive standard deviations; I wouldn't expect a membrane
> to
> fluctuate quite that much. Are you averaging only the z-component of the
> distance?
>
> > Is it normal, that I’m getting a higher thickness at higher temperature?
> Or are my results are ‘ok', considering the values of both standard
> deviation?
>
> Your results are indistinguishable, given the huge standard deviations.
>
> -Justin
>
> > In any case; I think this is strange, because using a different
> approximation/methods (GridMAT-MD) i got at 300K, d= 3.996 and at 329K d=
> 3.869 ( more ‘normal’ results for this type of lipid at this temperatures).
> > Am i missing something with my approximation that is 'disrupting' my
> results?
> > I’ll prefer to use gmx distance to analyse d in my simulations,
> considering the extensive amount of time that will take me if i use
> GridMAT-MD to analyse my 1us of production data.
> > Any thoughts/suggestions are more than welcome.
> > Best,
> > Carlos
> >
> >
> > --
> > Carlos Navarro Retamal
> > Bioinformatics Engineering
> > Ph. D (c) Applied Sciences.
> > Center of Bioinformatics and Molecular Simulations. CBSM
> > University of Talca
> > Av. Lircay S/N, Talca, Chile
> > T: (+56) 712201 798
> > E: carlos.navarr...@gmail.com or cnava...@utalca.cl
> >
>
> --
> 

[gmx-users] Question about redundancy in forcefield files and dihedral parameterization

[Eric Smoll]

Hello GROMACS users,

In the *types directives, what impact does redundancy have? Does a later
specification  override an earlier specification? For a concrete example,
consider a bondtypes entry:
[ bondtypes ]
A B 1 1.0 2.0
A B 1 1.0 3.0
Which specification will be used?

What impact does arrangement redundancy have on dihedral parameters? Will
the equivalent specifications shown below cause problems?
[ dihedraltypes ]
A B B C 3 1.0 2.0 3.0 4.0  5.0 6.0
C B B A 3 1.0 2.0 3.0 4.0  5.0 6.0
C B B A 3 1.0 2.0 3.0 4.0  5.0 600.0

When computing dihedral parameters of small symmetric molecules using ab
initio calculations, does one divide the weight or amplitude of the
LJ-subtracted dihedral potential across equivalent dihedrals along the same
bond? For example, does the computed dihedral spectrum of ethane (H-C-C-H)
get divided by 9?

Best,
Eric
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[gmx-users] performance of e5 2630 CPU with gtx-titan GPU

[Netaly Khazanov]

Hello All,
Does anybody know what is the performance of this combination of CPU and
GPU?

Thanks in advance.



-- 
Netaly
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Re: [gmx-users] Measuring Bilayer thickness with gmx distance in CGMD simulations

[Teemu Murtola]

Please upgrade to 5.0.6. There was a bug with gmx distance -oxyz that
caused the output file to not appear (or to overwrite some unintended
files), which was fixed for the latest version.

On Tue, Jul 28, 2015, 17:34 Carlos Navarro Retamal 
wrote:

> Hi Justin,
> thanks for your reply.
> Is there a way, to analyse each component (x,y,z) of the distance without
> the flag -oxyz?
> For some reason, I’m unable to get this data with gmx distance.
> In fact, when i ran
> gmx distance -f trajout329K.xtc -s POPC-329K-2us.tpr -n index.ndx -oxyz
> the command line doesn’t generate anything (any *xvg file).
> I don’t know what I’m doing wrong
> Best,
> Carlos
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
>
>
> On July 28, 2015 at 9:34:32 AM, Justin Lemkul (jalem...@vt.edu jalem...@vt.edu>) wrote:
>
> July 28, 2015 at 6:09:51 AM GMT-3 ro Retamal wrote:
> > Dear gmx users,
> > I’m studying the implication of higher temperatures in the membrane
> thickness (d) of several bilayer during CGMD simulations.
> > In order to measure d in a pure POPC membrane i create an index group
> containing only PO4 beads.
> > Before everything, i remove PBC conditions in the simulations as
> following:
> > trjconv -f POPC-300K-2us.xtc -s POPC-300K-2us.tpr -pbc nojump -o
> trajout300K.xtc
> > trjconv -f POPC-329K-2us.xtc -s POPC-329K-2us.tpr -pbc nojump -o
> trajout329K.xtc
> >
> > Then, I used gmx distance:
> > gmx distance -f trajout300K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav
> avg-300K
> > gmx distance -f trajout329K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav
> avg-329K
> >
> > Finally, using g_analyse i analyse both *xvg files and i got:
> >
> > 300K:
> > Average distance: 4.090 nm
> > Standard deviation: 1.451 nm
> >
> > 329K:
> > Average distance: 4.134 nm
> > Standard deviation: 1.515 nm
> >
>
> Those are pretty massive standard deviations; I wouldn't expect a membrane
> to
> fluctuate quite that much. Are you averaging only the z-component of the
> distance?
>
> > Is it normal, that I’m getting a higher thickness at higher temperature?
> Or are my results are ‘ok', considering the values of both standard
> deviation?
>
> Your results are indistinguishable, given the huge standard deviations.
>
> -Justin
>
> > In any case; I think this is strange, because using a different
> approximation/methods (GridMAT-MD) i got at 300K, d= 3.996 and at 329K d=
> 3.869 ( more ‘normal’ results for this type of lipid at this temperatures).
> > Am i missing something with my approximation that is 'disrupting' my
> results?
> > I’ll prefer to use gmx distance to analyse d in my simulations,
> considering the extensive amount of time that will take me if i use
> GridMAT-MD to analyse my 1us of production data.
> > Any thoughts/suggestions are more than welcome.
> > Best,
> > Carlos
> >
> >
> > --
> > Carlos Navarro Retamal
> > Bioinformatics Engineering
> > Ph. D (c) Applied Sciences.
> > Center of Bioinformatics and Molecular Simulations. CBSM
> > University of Talca
> > Av. Lircay S/N, Talca, Chile
> > T: (+56) 712201 798
> > E: carlos.navarr...@gmail.com or cnava...@utalca.cl
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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Re: [gmx-users] (no subject)

[Sotirios Dionysios I. Papadatos]

This is most probably due to some missing atoms. If you are not trying to 
include "exotic" atoms, meaning that you have to add them to aminoacids.rtp etc 
then you need a program like "Schrodinger/maestro" to manually add the atoms 
missing, export it to .pdb and try again.
Hope that helps


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of hari ram 

Sent: Monday, July 27, 2015 2:04 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] (no subject)

Hi Users,

I have a .pdb file, in this file when I want to use pdb2gmx command there is 
this error massage:Fatal error:
Incomplete ring in HIS771

this aminoacid is not complete in general, I don't know how can I
complete this such that I don't add HIS for complete? Please give me a
hint.


Thank you

Hari

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Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0

[Eudes Fileti]

Dear Chris, thank you for help. I performed the test you suggested, with no
pressure coupling. Note that the behavior of the profile remained the same
even with no pressure coupling.
https://goo.gl/photos/2d8tsYFwp2eHCuCWA

The simulation parameters were exactly the same (except the sampling in the
test was 5 ns window and by coupling pressure, which was turned off).

Bests
eef

___
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Página: sites.google.com/site/fileti/


> --
>
> Message: 2
> Date: Sun, 26 Jul 2015 02:45:50 +
> From: Christopher Neale 
> To: "gmx-us...@gromacs.org" 
> Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0
> (Eudes  Fileti)
> Message-ID:
> <
> blupr03mb184037e6ef2ec6d63bebe21c5...@blupr03mb184.namprd03.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Eudes:
>
> Glad that you solved one of the two issues. As for the bumps in the PMF, I
> have a new theory: the bumps come from pressure coupling. When the sampled
> distance, d, between the two molecules fluctuate a little closer than the
> center of restraint, d0, that adds a repulsive force that contributes to
> the virial and the box gets a little larger. Conversely, slight
> fluctuations of d that are larger than d0 will add a small bias to box
> contraction. This should be more noticeable when the restrained distance
> involves larger masses.
>
> It is at the moment unclear to me whether this might exert an effect
> indirectly due to overall system density or more directly as coordinate
> scaling impacts the instantaneous value of d. If it is the latter, then
> semi-isotropic pressure coupling, may also enhance the effect since the
> virial will be computed independently along the order parameter (I presume)
> and hence there is less noise from other dimensions.
>
> Can you please try again without pressure coupling (single precision
> should be fine for this test). Hopefully this is not the source of the
> bumps because, if it is affecting the PMF noticeably and the underlying
> free energy surface has a large gradient, then d will always be on one side
> of d0 and the effect will not be merely bumps but also some type of bias in
> the PMF. Whether this bias is accurate or artifactual falls outside of my
> mathematical abilities. The thing is, the force is a real force between
> real atoms so it seems like it really should be included in the virial (as
> it certainly is... I checked). I can tell you one thing for sure: the
> effect on box volume is real and noticeable. That is, if you look at the
> average system volume when d< manner from the average system volume when d>>d0 (something that I also
> checked).
>
> Thank you for looking into this further,
> Chris.
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Eudes
> Fileti 
> Sent: 24 July 2015 16:47
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0
> (Eudes Fileti)
>
> Hello Chris, I write to report the results of the tests you suggested.
> To recap, I have two problems to solve. 1) The bad sampling around z = 0
> and 2) the bumps along to the profile.
>
> I solved the first discarding all the my initial configurations and
> performing a new pulling (SMD). Only this time I used a higher force
> constant (5000 kJ/mol nm2). Thus I got configurations close to z = 0, where
> they were not generated.
>
> For the second problem, you suggested recalculate the PMF using double
> precision. The results of this test showed that it does not solve the
> problem, on the contrary the bumps were even more pronounced, as indicated
> by the plot in this link. https://goo.gl/photos/wGNhdyNG9pdqGfcB6
>
> All tests were performed with prototypes simulations, with 40 windows of 2
> ns spaced by 0.1 nm. A larger sample is obviously necessary for reliable
> profiles, but this was enough to show the trend that I wanted to watch.
>
> As I have mentioned before, I've done several tests aiming to eliminate
> these bumps: use of higher sampling, up to 20ns per window; reducing the
> spacing between the windows (from 0.1 to 0.05 nm); changing the spring
> constant from 1000 up to 5000 kJ/mol nm2, use of two different versions of
> the Gromacs (4.6 e 5.0) and also I tested it with two different sets of
> initial settings.
>
> None of this attempts solved the bumps problem.
>
> If you (or someone else) have any other tips please let me know.
>
> Thank you
> eef
>
> ___
> Eudes Eterno Fileti
> Instituto de Ci?ncia e Tecnologia da UNIFESP
> Rua Talim, 330, S?o Jos? dos Campos - SP
> P?gina: sites.google.com/site/fileti/
>
> >
> > --
> >
> > Message: 4
> > Date: We

Re: [gmx-users] Are water molecules restrained "by default"?

[Dawid das]

Thank you! :)

2015-07-28 15:30 GMT+01:00 Justin Lemkul :

>
>
> On 7/28/15 10:16 AM, Dawid das wrote:
>
>> 2015-07-28 15:02 GMT+01:00 Justin Lemkul :
>>
>> Those are reference positions for restraints.  The restraints won't be
>>> applied to anything that's not actually specified in
>>> [position_restraints].
>>>
>>>
>>
>> Right, so that means that if I read all atoms in *trp file as I send you
>> in
>> my previous message but only heavy atoms indexes are present in posre.itp
>> file, it's all fine? Only those heavy ones are restrained?
>>
>>
> Yes.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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Re: [gmx-users] Measuring Bilayer thickness with gmx distance in CGMD simulations

[Carlos Navarro Retamal]

Hi Justin,
thanks for your reply.
Is there a way, to analyse each component (x,y,z) of the distance without the 
flag -oxyz?
For some reason, I’m unable to get this data with gmx distance.
In fact, when i ran
gmx distance -f trajout329K.xtc -s POPC-329K-2us.tpr -n index.ndx -oxyz
the command line doesn’t generate anything (any *xvg file).
I don’t know what I’m doing wrong
Best,
Carlos
--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarr...@gmail.com or cnava...@utalca.cl



On July 28, 2015 at 9:34:32 AM, Justin Lemkul 
(jalem...@vt.edu) wrote:

July 28, 2015 at 6:09:51 AM GMT-3 ro Retamal wrote:
> Dear gmx users,
> I’m studying the implication of higher temperatures in the membrane thickness 
> (d) of several bilayer during CGMD simulations.
> In order to measure d in a pure POPC membrane i create an index group 
> containing only PO4 beads.
> Before everything, i remove PBC conditions in the simulations as following:
> trjconv -f POPC-300K-2us.xtc -s POPC-300K-2us.tpr -pbc nojump -o 
> trajout300K.xtc
> trjconv -f POPC-329K-2us.xtc -s POPC-329K-2us.tpr -pbc nojump -o 
> trajout329K.xtc
>
> Then, I used gmx distance:
> gmx distance -f trajout300K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav 
> avg-300K
> gmx distance -f trajout329K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav 
> avg-329K
>
> Finally, using g_analyse i analyse both *xvg files and i got:
>
> 300K:
> Average distance: 4.090 nm
> Standard deviation: 1.451 nm
>
> 329K:
> Average distance: 4.134 nm
> Standard deviation: 1.515 nm
>

Those are pretty massive standard deviations; I wouldn't expect a membrane to
fluctuate quite that much. Are you averaging only the z-component of the 
distance?

> Is it normal, that I’m getting a higher thickness at higher temperature? Or 
> are my results are ‘ok', considering the values of both standard deviation?

Your results are indistinguishable, given the huge standard deviations.

-Justin

> In any case; I think this is strange, because using a different 
> approximation/methods (GridMAT-MD) i got at 300K, d= 3.996 and at 329K d= 
> 3.869 ( more ‘normal’ results for this type of lipid at this temperatures).
> Am i missing something with my approximation that is 'disrupting' my results?
> I’ll prefer to use gmx distance to analyse d in my simulations, considering 
> the extensive amount of time that will take me if i use GridMAT-MD to analyse 
> my 1us of production data.
> Any thoughts/suggestions are more than welcome.
> Best,
> Carlos
>
>
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
>

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Are water molecules restrained "by default"?

[Justin Lemkul]

On 7/28/15 10:16 AM, Dawid das wrote:

2015-07-28 15:02 GMT+01:00 Justin Lemkul :


Those are reference positions for restraints.  The restraints won't be
applied to anything that's not actually specified in [position_restraints].




Right, so that means that if I read all atoms in *trp file as I send you in
my previous message but only heavy atoms indexes are present in posre.itp
file, it's all fine? Only those heavy ones are restrained?



Yes.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Are water molecules restrained "by default"?

[Dawid das]

2015-07-28 15:02 GMT+01:00 Justin Lemkul :

> Those are reference positions for restraints.  The restraints won't be
> applied to anything that's not actually specified in [position_restraints].
>


Right, so that means that if I read all atoms in *trp file as I send you in
my previous message but only heavy atoms indexes are present in posre.itp
file, it's all fine? Only those heavy ones are restrained?
-- 
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Re: [gmx-users] Are water molecules restrained "by default"?

[Justin Lemkul]

On 7/28/15 10:00 AM, Dawid das wrote:

Thank you, but I am still pretty confused. In my *mdp file I use
define = -DPOSRES

and in my *top file there is:

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

now in posre.itp file there are ONLY non-hydrogen atoms of protein.
However after running grompp and using gmxdump to read *trp file I can see:

topology:
name="RIBONUCLEASE A in water"
#atoms   = 25205
#molblock= 4
molblock (0):
   moltype  = 0 "Protein_chain_A"
   #molecules   = 1
   #atoms_mol   = 1858
   #posres_xA   = 1858
   posres_xA (1858x3):
  posres_xA[0]={ 3.10600e+00,  1.16400e+00,  2.92300e+00}
  posres_xA[1]={ 3.04300e+00,  1.09500e+00,  2.88800e+00}
  posres_xA[2]={ 3.16400e+00,  1.19800e+00,  2.84900e+00}
  posres_xA[3]={ 3.16400e+00,  1.12300e+00,  2.99400e+00}
  posres_xA[4]={ 3.02900e+00,  1.27700e+00,  2.98200e+00}


and ALL of the atoms of the protein. In fact, there are 1858 of them, so
also hydrogen atoms are restrained.


Those are reference positions for restraints.  The restraints won't be applied 
to anything that's not actually specified in [position_restraints].



Why? These lines:
#ifdef POSRES
#include "posre.itp"
#endif

are under topology definition of the whole protein:
[ moleculetype ]
; Namenrexcl
Protein_chain_A 3

[ atoms ]

Although I read documentation on your website I do not understand how I can
create [ moleculetype ] for the non-hydrogen atoms only.



You don't need to.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Re: [gmx-users] Are water molecules restrained "by default"?

[Dawid das]

Thank you, but I am still pretty confused. In my *mdp file I use
define = -DPOSRES

and in my *top file there is:

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

now in posre.itp file there are ONLY non-hydrogen atoms of protein.
However after running grompp and using gmxdump to read *trp file I can see:

topology:
   name="RIBONUCLEASE A in water"
   #atoms   = 25205
   #molblock= 4
   molblock (0):
  moltype  = 0 "Protein_chain_A"
  #molecules   = 1
  #atoms_mol   = 1858
  #posres_xA   = 1858
  posres_xA (1858x3):
 posres_xA[0]={ 3.10600e+00,  1.16400e+00,  2.92300e+00}
 posres_xA[1]={ 3.04300e+00,  1.09500e+00,  2.88800e+00}
 posres_xA[2]={ 3.16400e+00,  1.19800e+00,  2.84900e+00}
 posres_xA[3]={ 3.16400e+00,  1.12300e+00,  2.99400e+00}
 posres_xA[4]={ 3.02900e+00,  1.27700e+00,  2.98200e+00}


and ALL of the atoms of the protein. In fact, there are 1858 of them, so
also hydrogen atoms are restrained.
Why? These lines:
#ifdef POSRES
#include "posre.itp"
#endif

are under topology definition of the whole protein:
[ moleculetype ]
; Namenrexcl
Protein_chain_A 3

[ atoms ]

Although I read documentation on your website I do not understand how I can
create [ moleculetype ] for the non-hydrogen atoms only.

Best wishes,

Dawid Grabarek

2015-07-27 22:25 GMT+01:00 Justin Lemkul :

>
>
> On 7/27/15 5:18 PM, Dawid das wrote:
>
>> Dear Gromacs Experts,
>>
>> I read in Gromacs documentation that
>> #POSRES_WATER
>> will be interpreted to restrain position of all water oxygen atoms.
>> However
>> if I understand it correctly I should define where proper *itp file is
>> present as it is for restraining heavy atoms of my protein molecule:
>>
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> I neither use #include mechanism for water oxygens nor #define.
>> However I do not get any errors as the documentation suggest when
>> POSRES_WATER is not defined.
>> So my question is whether using this what grompp has generated regarding
>> restraining water oxygens:
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct   fcxfcyfcz
>> 11   1000   1000   1000
>> #endif
>>
>> is enough to actually restrain those atoms? Or my atoms are not restrained
>> after all?
>> However if they are, how does Gromacs know what atoms are water oxygen
>> atoms? Simply it "recognizes" them because POSRES_WATER flag is used and
>> somewhere in my *top file I include *itp file for water molecues:
>> #include "charmm27.ff/tip3p.itp"
>> ?
>>
>>
> Whether or not restraints are applied is dependent upon what you use in
> the .mdp file with the "define" keyword.  See the manual and basic
> tutorials.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Regarding engineered residue topology

[Justin Lemkul]

On 7/28/15 8:48 AM, Venkat Reddy wrote:

Thanks Justin. How shall I tackle this problem? Can I use any other AA
force field, say CHARMM27?


Use any force field you like that has suitable parameters and will adequately 
address the desired simulation.



The Aib parameters are available in an old gromacs forcefield (mentioned as
"DEPRECATED" in gromacs-4.5.7), which hasn't showed any error while
simulating the same system.



One should not use ffgmx (hacked GROMOS87, not to be called "GROMACS force 
field," even though people unfortunately do).


-Justin


On Tue, Jul 28, 2015 at 6:07 PM, Justin Lemkul  wrote:




On 7/28/15 3:30 AM, Venkat Reddy wrote:


Thank you Justin for clear explanation.
However, the parameters are available for
CX CT CT_2   HC  3  0.96650   2.89951   0.0  -3.86601
0.000   0.000;
C* CT CT_2   HC  3  0.96650   2.89951   0.0  -3.86601
0.000   0.000 ;
So, can I apply the same for CT-CT_2-CT-HC dihedral?



No idea.  Generally dihedrals are the least transferable of any bonded
parameter, so there's no reason to assume that you can apply the parameters
from other interactions to any other given interaction.

-Justin


  Thank you for your valuable time and concern.


On Mon, Jul 27, 2015 at 5:16 PM, Justin Lemkul  wrote:




On 7/27/15 1:21 AM, Venkat Reddy wrote:

  Dear Justin,

Thank you for the prompt reply. I have checked the topology file once
again
and confirmed the dihedral (CB2-CA-CB1-HB11) thats creating problem. The
Aib parameters are indeed available for OPLS-AA ff. But I couldn't
locate
the dihedral parameters for the above mentioned dihedral angle in
ffbonded.itp file. However I found dihedral parameters for X-CA-CB-X.
So,
can I use X-CA-CB-X parameters for CB2-CA-CB1-HB11 dihedral?


  You're confusing atom names and atom types.  The names are totally

irrelevant for parameter assignment.  The CB2-C1-CB1-HB11 dihedral has a
sequence of nonbonded types of opls_135-opls_225B-opls_135-opls_140,
which
have bonded types (see second column of ffnonbonded.itp) of
CT-CT_2-CT-HC.
So the parameters you need are for CT-CT_2-CT-HC, which are indeed not in
ffbonded.itp.

-Justin


   On Mon, Jul 27, 2015 at 5:46 AM, Justin Lemkul 
wrote:






On 7/24/15 9:20 AM, Venkat Reddy wrote:

   Dear all,


I am trying to simulate a peptide with engineered residues like Aib
(alpha
amino-isobutyric acid). I am trying to use OPLS-aa forcefield. Though
everything went well initially during topology generation, grompp
showed
the following error.

ERROR 1 [file topol.top, line 2316]:
  No default Ryckaert-Bell. types
ERROR 2 [file topol.top, line 2317]:
  No default Ryckaert-Bell. types
ERROR 3 [file topol.top, line 2318]:
  No default Ryckaert-Bell. types
ERROR 4 [file topol.top, line 2325]:
  No default Ryckaert-Bell. types
ERROR 5 [file topol.top, line 2326]:
  No default Ryckaert-Bell. types
ERROR 6 [file topol.top, line 2327]:
  No default Ryckaert-Bell. types

The cross-check with topolo.top identified the dihedral
CB2-CA-CB1-HB11
is
throwing the error. My question is, even though the parameters for Aib
are
available in OPLS ff, why I am getting this error?


   grompp doesn't lie.  Either you're looking at the wrong lines or
you're


looking at the wrong parameters.  Some residues are constructed for
convenience but if they're not "official" then there may be problems.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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  --

==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Re: [gmx-users] problem with kalp simulation in DPPC

[Justin Lemkul]

On 7/28/15 8:18 AM, fatemeh wrote:

Hello

I am  a new user of gromacs. i have two problems while practicing
simulation of  Kalp15 in DPPC Dr Justine Lemkul tutorial

i have problem with this part

"genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10

In the .mdp file used for the minimizations, add a line "define = -
DSTRONG_POSRES" to make use of these new position restraints. Then, simply
follow the InflateGRO instructions (contained in the script itself), a
procedure that is easily scripted. Scale the lipid positions by a factor
of 4:

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat"

first i cannot find  InflateGRO instructions


That's what the above command is.


and i want to know whether i should follow all of the steps or not


Tutorial steps are not optional.  Follow them exactly.


and when should i execute this command?


When the tutorial tells you to.

-Justin


perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

after doing InflateGRO instructions?



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0

[Christopher Neale]

Dear Eudes:

then I return to being stumped. It sure looks like it might be an issue with a 
constant somewhere. I'll note that v5.0.5 g_wham uses what I think is an 
incorrect constant to convert to kcal (http://redmine.gromacs.org/issues/1787), 
but you're using kj so that shouldn't be it. The gas constant defined by g_wham 
on line 1086 in v5.0.5 is also a little bit different from the one used in core 
gromacs (for e.g. replica exchange to get the boltzmann constant), though again 
I don't see how this could do anything but affect the overall scale by a tiny 
amount.

However, I do wonder about "8.314e-3" in lines like this where it possibly 
could affect the value:
denom += invg*window[j].N[k]*exp(-U/(8.314e-3*opt->Temperature) 
+ window[j].z[k]);
(line 966 in calc_profile() in v5.0.5)

Are you using g_wham? Can you try a different wham software and see if you get 
the same thing?

Also, are you setting -temp properly in g_wham ?

Beyond that, I've run out of ideas. If you do ever sort this out, I'd 
appreciate it if you could send me an email off list to let me know (and post 
it here of course, I just don't always check the list).

Thank you,
Chris.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Eudes Fileti 

Sent: 28 July 2015 07:59
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0

Dear Chris, thank you for help. I performed the test you suggested, with no
pressure coupling. Note that the behavior of the profile remained the same
even with no pressure coupling.
https://goo.gl/photos/2d8tsYFwp2eHCuCWA

The simulation parameters were exactly the same (except the sampling in the
test was 5 ns window and by coupling pressure, which was turned off).

Bests
eef

___
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Página: sites.google.com/site/fileti/


> --
>
> Message: 2
> Date: Sun, 26 Jul 2015 02:45:50 +
> From: Christopher Neale 
> To: "gmx-us...@gromacs.org" 
> Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0
> (Eudes  Fileti)
> Message-ID:
> <
> blupr03mb184037e6ef2ec6d63bebe21c5...@blupr03mb184.namprd03.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Eudes:
>
> Glad that you solved one of the two issues. As for the bumps in the PMF, I
> have a new theory: the bumps come from pressure coupling. When the sampled
> distance, d, between the two molecules fluctuate a little closer than the
> center of restraint, d0, that adds a repulsive force that contributes to
> the virial and the box gets a little larger. Conversely, slight
> fluctuations of d that are larger than d0 will add a small bias to box
> contraction. This should be more noticeable when the restrained distance
> involves larger masses.
>
> It is at the moment unclear to me whether this might exert an effect
> indirectly due to overall system density or more directly as coordinate
> scaling impacts the instantaneous value of d. If it is the latter, then
> semi-isotropic pressure coupling, may also enhance the effect since the
> virial will be computed independently along the order parameter (I presume)
> and hence there is less noise from other dimensions.
>
> Can you please try again without pressure coupling (single precision
> should be fine for this test). Hopefully this is not the source of the
> bumps because, if it is affecting the PMF noticeably and the underlying
> free energy surface has a large gradient, then d will always be on one side
> of d0 and the effect will not be merely bumps but also some type of bias in
> the PMF. Whether this bias is accurate or artifactual falls outside of my
> mathematical abilities. The thing is, the force is a real force between
> real atoms so it seems like it really should be included in the virial (as
> it certainly is... I checked). I can tell you one thing for sure: the
> effect on box volume is real and noticeable. That is, if you look at the
> average system volume when d< manner from the average system volume when d>>d0 (something that I also
> checked).
>
> Thank you for looking into this further,
> Chris.
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Eudes
> Fileti 
> Sent: 24 July 2015 16:47
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0
> (Eudes Fileti)
>
> Hello Chris, I write to report the results of the tests you suggested.
> To recap, I have two problems to solve. 1) The bad sampling around z = 0
> and 2) the bumps along to the profile.
>
> I solved the first discarding all the my initial configurations and
> performing a new pulling (SMD). Only t

Re: [gmx-users] Regarding engineered residue topology

[Venkat Reddy]

Thanks Justin. How shall I tackle this problem? Can I use any other AA
force field, say CHARMM27?
The Aib parameters are available in an old gromacs forcefield (mentioned as
"DEPRECATED" in gromacs-4.5.7), which hasn't showed any error while
simulating the same system.

On Tue, Jul 28, 2015 at 6:07 PM, Justin Lemkul  wrote:

>
>
> On 7/28/15 3:30 AM, Venkat Reddy wrote:
>
>> Thank you Justin for clear explanation.
>> However, the parameters are available for
>> CX CT CT_2   HC  3  0.96650   2.89951   0.0  -3.86601
>> 0.000   0.000;
>> C* CT CT_2   HC  3  0.96650   2.89951   0.0  -3.86601
>> 0.000   0.000 ;
>> So, can I apply the same for CT-CT_2-CT-HC dihedral?
>>
>>
> No idea.  Generally dihedrals are the least transferable of any bonded
> parameter, so there's no reason to assume that you can apply the parameters
> from other interactions to any other given interaction.
>
> -Justin
>
>
>  Thank you for your valuable time and concern.
>>
>> On Mon, Jul 27, 2015 at 5:16 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/27/15 1:21 AM, Venkat Reddy wrote:
>>>
>>>  Dear Justin,
 Thank you for the prompt reply. I have checked the topology file once
 again
 and confirmed the dihedral (CB2-CA-CB1-HB11) thats creating problem. The
 Aib parameters are indeed available for OPLS-AA ff. But I couldn't
 locate
 the dihedral parameters for the above mentioned dihedral angle in
 ffbonded.itp file. However I found dihedral parameters for X-CA-CB-X.
 So,
 can I use X-CA-CB-X parameters for CB2-CA-CB1-HB11 dihedral?


  You're confusing atom names and atom types.  The names are totally
>>> irrelevant for parameter assignment.  The CB2-C1-CB1-HB11 dihedral has a
>>> sequence of nonbonded types of opls_135-opls_225B-opls_135-opls_140,
>>> which
>>> have bonded types (see second column of ffnonbonded.itp) of
>>> CT-CT_2-CT-HC.
>>> So the parameters you need are for CT-CT_2-CT-HC, which are indeed not in
>>> ffbonded.itp.
>>>
>>> -Justin
>>>
>>>
>>>   On Mon, Jul 27, 2015 at 5:46 AM, Justin Lemkul 
>>> wrote:
>>>



> On 7/24/15 9:20 AM, Venkat Reddy wrote:
>
>   Dear all,
>
>> I am trying to simulate a peptide with engineered residues like Aib
>> (alpha
>> amino-isobutyric acid). I am trying to use OPLS-aa forcefield. Though
>> everything went well initially during topology generation, grompp
>> showed
>> the following error.
>>
>> ERROR 1 [file topol.top, line 2316]:
>>  No default Ryckaert-Bell. types
>> ERROR 2 [file topol.top, line 2317]:
>>  No default Ryckaert-Bell. types
>> ERROR 3 [file topol.top, line 2318]:
>>  No default Ryckaert-Bell. types
>> ERROR 4 [file topol.top, line 2325]:
>>  No default Ryckaert-Bell. types
>> ERROR 5 [file topol.top, line 2326]:
>>  No default Ryckaert-Bell. types
>> ERROR 6 [file topol.top, line 2327]:
>>  No default Ryckaert-Bell. types
>>
>> The cross-check with topolo.top identified the dihedral
>> CB2-CA-CB1-HB11
>> is
>> throwing the error. My question is, even though the parameters for Aib
>> are
>> available in OPLS ff, why I am getting this error?
>>
>>
>>   grompp doesn't lie.  Either you're looking at the wrong lines or
>> you're
>>
> looking at the wrong parameters.  Some residues are constructed for
> convenience but if they're not "official" then there may be problems.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>
>


  --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ===

[gmx-users] on MD simulation of ATP hydrolysis driven protein conformational change

[Brett]

Dear All,


There are some biological processes involving ATP hydrolysis driven protein 
conformational change. By MD, can we simulate the protein global conformational 
change driven by ATP hydrolysis? Or by MD can we investigate how the energy 
stored in ATP converts to protein conformational change?


Brett
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Re: [gmx-users] Regarding engineered residue topology

[Justin Lemkul]

On 7/28/15 3:30 AM, Venkat Reddy wrote:

Thank you Justin for clear explanation.
However, the parameters are available for
CX CT CT_2   HC  3  0.96650   2.89951   0.0  -3.86601
0.000   0.000;
C* CT CT_2   HC  3  0.96650   2.89951   0.0  -3.86601
0.000   0.000 ;
So, can I apply the same for CT-CT_2-CT-HC dihedral?



No idea.  Generally dihedrals are the least transferable of any bonded 
parameter, so there's no reason to assume that you can apply the parameters from 
other interactions to any other given interaction.


-Justin


Thank you for your valuable time and concern.

On Mon, Jul 27, 2015 at 5:16 PM, Justin Lemkul  wrote:




On 7/27/15 1:21 AM, Venkat Reddy wrote:


Dear Justin,
Thank you for the prompt reply. I have checked the topology file once
again
and confirmed the dihedral (CB2-CA-CB1-HB11) thats creating problem. The
Aib parameters are indeed available for OPLS-AA ff. But I couldn't locate
the dihedral parameters for the above mentioned dihedral angle in
ffbonded.itp file. However I found dihedral parameters for X-CA-CB-X. So,
can I use X-CA-CB-X parameters for CB2-CA-CB1-HB11 dihedral?



You're confusing atom names and atom types.  The names are totally
irrelevant for parameter assignment.  The CB2-C1-CB1-HB11 dihedral has a
sequence of nonbonded types of opls_135-opls_225B-opls_135-opls_140, which
have bonded types (see second column of ffnonbonded.itp) of CT-CT_2-CT-HC.
So the parameters you need are for CT-CT_2-CT-HC, which are indeed not in
ffbonded.itp.

-Justin


  On Mon, Jul 27, 2015 at 5:46 AM, Justin Lemkul  wrote:





On 7/24/15 9:20 AM, Venkat Reddy wrote:

  Dear all,

I am trying to simulate a peptide with engineered residues like Aib
(alpha
amino-isobutyric acid). I am trying to use OPLS-aa forcefield. Though
everything went well initially during topology generation, grompp showed
the following error.

ERROR 1 [file topol.top, line 2316]:
 No default Ryckaert-Bell. types
ERROR 2 [file topol.top, line 2317]:
 No default Ryckaert-Bell. types
ERROR 3 [file topol.top, line 2318]:
 No default Ryckaert-Bell. types
ERROR 4 [file topol.top, line 2325]:
 No default Ryckaert-Bell. types
ERROR 5 [file topol.top, line 2326]:
 No default Ryckaert-Bell. types
ERROR 6 [file topol.top, line 2327]:
 No default Ryckaert-Bell. types

The cross-check with topolo.top identified the dihedral CB2-CA-CB1-HB11
is
throwing the error. My question is, even though the parameters for Aib
are
available in OPLS ff, why I am getting this error?


  grompp doesn't lie.  Either you're looking at the wrong lines or you're

looking at the wrong parameters.  Some residues are constructed for
convenience but if they're not "official" then there may be problems.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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send a mail to gmx-users-requ...@gromacs.org.







--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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send a mail to gmx-users-requ...@gromacs.org.







--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Measuring Bilayer thickness with gmx distance in CGMD simulations

[Justin Lemkul]

On 7/28/15 1:01 AM, Carlos Navarro Retamal wrote:

Dear gmx users,
I’m studying the implication of higher temperatures in the membrane thickness 
(d) of several bilayer during CGMD simulations.
In order to measure d in a pure POPC membrane i create an index group 
containing only PO4 beads.
Before everything, i remove PBC conditions in the simulations as following:
trjconv -f POPC-300K-2us.xtc -s POPC-300K-2us.tpr -pbc nojump -o trajout300K.xtc
trjconv -f POPC-329K-2us.xtc -s POPC-329K-2us.tpr -pbc nojump -o trajout329K.xtc

Then, I used gmx distance:
gmx distance -f trajout300K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav avg-300K
gmx distance -f trajout329K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav avg-329K

Finally, using g_analyse i analyse both *xvg files and i got:

300K:
Average distance:   4.090  nm
Standard deviation: 1.451  nm

329K:
Average distance:   4.134  nm
Standard deviation: 1.515  nm



Those are pretty massive standard deviations; I wouldn't expect a membrane to 
fluctuate quite that much.  Are you averaging only the z-component of the distance?



Is it normal, that I’m getting a higher thickness at higher temperature? Or are 
my results are ‘ok', considering the values of both standard deviation?


Your results are indistinguishable, given the huge standard deviations.

-Justin


In any case; I think this is strange, because using a different 
approximation/methods  (GridMAT-MD) i got at 300K, d= 3.996 and at 329K d= 
3.869 ( more ‘normal’ results for this type of lipid at this temperatures).
Am i missing something with my approximation that is 'disrupting' my results?
I’ll prefer to use gmx distance to analyse d in my simulations, considering the 
extensive amount of time that will take me if i use GridMAT-MD to analyse my 
1us of production data.
Any thoughts/suggestions are more than welcome.
Best,
Carlos


--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarr...@gmail.com or cnava...@utalca.cl



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] relative constraint deviation after LINCS

[Pallavi Banerjee]

Hello Users,

I am carrying out simulated annealing of Polyacrylamide melt (NPT ensemble)
consisting of polymer chains of length 60; taking the temperature up from
400 K to 950 K and beating it down again. I do this in intervals of 50 K,
alternating between heating over 2 ns and equilibration for 3 ns, for a
total run time of 68 ns. What confounds me is that if I use OPLS as the
force field, it's a smooth error-free run but on using GROMOS, the LINCS
warning: "relative constraint deviation after LINCS" shows up after a
significant amount of run, (20-30 ns). I do not really understand the
force-field dependency here. Could someone throw some light on this?

Thanks,

Pallavi Banerjee.
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[gmx-users] problem with kalp simulation in DPPC

[fatemeh]

Hello

I am  a new user of gromacs. i have two problems while practicing 
simulation of  Kalp15 in DPPC Dr Justine Lemkul tutorial

i have problem with this part

"genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10

In the .mdp file used for the minimizations, add a line "define = -
DSTRONG_POSRES" to make use of these new position restraints. Then, simply 
follow the InflateGRO instructions (contained in the script itself), a 
procedure that is easily scripted. Scale the lipid positions by a factor 
of 4:

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat"

first i cannot find  InflateGRO instructions
and i want to know whether i should follow all of the steps or not
and when should i execute this command?
perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
 
after doing InflateGRO instructions?

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Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0

[Eudes Fileti]

Dear Chris, thank you for help. I performed the test you suggested, with no
pressure coupling. Note that the behavior of the profile remained the same
even with no pressure coupling.
https://goo.gl/photos/2d8tsYFwp2eHCuCWA

The simulation parameters were exactly the same (except the sampling in the
test was 5 ns window and by coupling pressure, which was turned off).

Bests
eef

___
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Página: sites.google.com/site/fileti/


> --
>
> Message: 2
> Date: Sun, 26 Jul 2015 02:45:50 +
> From: Christopher Neale 
> To: "gmx-us...@gromacs.org" 
> Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0
> (Eudes  Fileti)
> Message-ID:
> <
> blupr03mb184037e6ef2ec6d63bebe21c5...@blupr03mb184.namprd03.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Eudes:
>
> Glad that you solved one of the two issues. As for the bumps in the PMF, I
> have a new theory: the bumps come from pressure coupling. When the sampled
> distance, d, between the two molecules fluctuate a little closer than the
> center of restraint, d0, that adds a repulsive force that contributes to
> the virial and the box gets a little larger. Conversely, slight
> fluctuations of d that are larger than d0 will add a small bias to box
> contraction. This should be more noticeable when the restrained distance
> involves larger masses.
>
> It is at the moment unclear to me whether this might exert an effect
> indirectly due to overall system density or more directly as coordinate
> scaling impacts the instantaneous value of d. If it is the latter, then
> semi-isotropic pressure coupling, may also enhance the effect since the
> virial will be computed independently along the order parameter (I presume)
> and hence there is less noise from other dimensions.
>
> Can you please try again without pressure coupling (single precision
> should be fine for this test). Hopefully this is not the source of the
> bumps because, if it is affecting the PMF noticeably and the underlying
> free energy surface has a large gradient, then d will always be on one side
> of d0 and the effect will not be merely bumps but also some type of bias in
> the PMF. Whether this bias is accurate or artifactual falls outside of my
> mathematical abilities. The thing is, the force is a real force between
> real atoms so it seems like it really should be included in the virial (as
> it certainly is... I checked). I can tell you one thing for sure: the
> effect on box volume is real and noticeable. That is, if you look at the
> average system volume when d< manner from the average system volume when d>>d0 (something that I also
> checked).
>
> Thank you for looking into this further,
> Chris.
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Eudes
> Fileti 
> Sent: 24 July 2015 16:47
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0
> (Eudes Fileti)
>
> Hello Chris, I write to report the results of the tests you suggested.
> To recap, I have two problems to solve. 1) The bad sampling around z = 0
> and 2) the bumps along to the profile.
>
> I solved the first discarding all the my initial configurations and
> performing a new pulling (SMD). Only this time I used a higher force
> constant (5000 kJ/mol nm2). Thus I got configurations close to z = 0, where
> they were not generated.
>
> For the second problem, you suggested recalculate the PMF using double
> precision. The results of this test showed that it does not solve the
> problem, on the contrary the bumps were even more pronounced, as indicated
> by the plot in this link. https://goo.gl/photos/wGNhdyNG9pdqGfcB6
>
> All tests were performed with prototypes simulations, with 40 windows of 2
> ns spaced by 0.1 nm. A larger sample is obviously necessary for reliable
> profiles, but this was enough to show the trend that I wanted to watch.
>
> As I have mentioned before, I've done several tests aiming to eliminate
> these bumps: use of higher sampling, up to 20ns per window; reducing the
> spacing between the windows (from 0.1 to 0.05 nm); changing the spring
> constant from 1000 up to 5000 kJ/mol nm2, use of two different versions of
> the Gromacs (4.6 e 5.0) and also I tested it with two different sets of
> initial settings.
>
> None of this attempts solved the bumps problem.
>
> If you (or someone else) have any other tips please let me know.
>
> Thank you
> eef
>
> ___
> Eudes Eterno Fileti
> Instituto de Ci?ncia e Tecnologia da UNIFESP
> Rua Talim, 330, S?o Jos? dos Campos - SP
> P?gina: sites.google.com/site/fileti/
>
> >
> > --
> >
> > Message: 4
> > Date: We

[gmx-users] Problem with Inflategro

[fatemeh]

Hello
I am a new user of gromacs.
Thanks to Mr Justine Lemkul because of his useful tutorials, Lysozyme in 
water and kalp15 in DPPC.
currently I am practicing kalp15 tutorial in DPPC, and now i have problem 
with this part:

"genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10

In the .mdp file used for the minimizations, add a line "define = -
DSTRONG_POSRES" to make use of these new position restraints. Then, simply 
follow the InflateGRO instructions (contained in the script itself), a 
procedure that is easily scripted. Scale the lipid positions by a factor 
of 4:

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat"

I did the first command genrestr, but now i have two problems:
1) i cannot find InflateGRO instructions online 
and i want to know wheather i should do all of its steps or not?

and 2) when i have done InflateGRO instructions, i have to execute the 
second command "perl"???


thank you very much
Razavi

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Re: [gmx-users] Regarding engineered residue topology

[Venkat Reddy]

Thank you Justin for clear explanation.
However, the parameters are available for
CX CT CT_2   HC  3  0.96650   2.89951   0.0  -3.86601
0.000   0.000;
C* CT CT_2   HC  3  0.96650   2.89951   0.0  -3.86601
0.000   0.000 ;
So, can I apply the same for CT-CT_2-CT-HC dihedral?

Thank you for your valuable time and concern.

On Mon, Jul 27, 2015 at 5:16 PM, Justin Lemkul  wrote:

>
>
> On 7/27/15 1:21 AM, Venkat Reddy wrote:
>
>> Dear Justin,
>> Thank you for the prompt reply. I have checked the topology file once
>> again
>> and confirmed the dihedral (CB2-CA-CB1-HB11) thats creating problem. The
>> Aib parameters are indeed available for OPLS-AA ff. But I couldn't locate
>> the dihedral parameters for the above mentioned dihedral angle in
>> ffbonded.itp file. However I found dihedral parameters for X-CA-CB-X. So,
>> can I use X-CA-CB-X parameters for CB2-CA-CB1-HB11 dihedral?
>>
>>
> You're confusing atom names and atom types.  The names are totally
> irrelevant for parameter assignment.  The CB2-C1-CB1-HB11 dihedral has a
> sequence of nonbonded types of opls_135-opls_225B-opls_135-opls_140, which
> have bonded types (see second column of ffnonbonded.itp) of CT-CT_2-CT-HC.
> So the parameters you need are for CT-CT_2-CT-HC, which are indeed not in
> ffbonded.itp.
>
> -Justin
>
>
>  On Mon, Jul 27, 2015 at 5:46 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/24/15 9:20 AM, Venkat Reddy wrote:
>>>
>>>  Dear all,
 I am trying to simulate a peptide with engineered residues like Aib
 (alpha
 amino-isobutyric acid). I am trying to use OPLS-aa forcefield. Though
 everything went well initially during topology generation, grompp showed
 the following error.

 ERROR 1 [file topol.top, line 2316]:
 No default Ryckaert-Bell. types
 ERROR 2 [file topol.top, line 2317]:
 No default Ryckaert-Bell. types
 ERROR 3 [file topol.top, line 2318]:
 No default Ryckaert-Bell. types
 ERROR 4 [file topol.top, line 2325]:
 No default Ryckaert-Bell. types
 ERROR 5 [file topol.top, line 2326]:
 No default Ryckaert-Bell. types
 ERROR 6 [file topol.top, line 2327]:
 No default Ryckaert-Bell. types

 The cross-check with topolo.top identified the dihedral CB2-CA-CB1-HB11
 is
 throwing the error. My question is, even though the parameters for Aib
 are
 available in OPLS ff, why I am getting this error?


  grompp doesn't lie.  Either you're looking at the wrong lines or you're
>>> looking at the wrong parameters.  Some residues are constructed for
>>> convenience but if they're not "official" then there may be problems.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
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>>> posting!
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>>>
>>>
>>
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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