[gmx-users] Question regarding error

[Marko Sever]

Why would such a command: 

gmx pdb2gmx -f system.pdb -i /home/bla/charmm36chol_psm_dopc.ff/PSM.itp -o 
systemprocessed.gro -water tip3p -ignh -ff charmm36chol_psm_dopc 

give me the following error:

Fatal error:
Residue 'PSM' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


If I pointed it to the PSM.itp file?
What is the procedure to manually add the includes into the .top and yet 
generate the .gro file of the system? Is there any alternative to pdb2gmx or 
should I use that...
I got .itp files for the system from Charmm GUI.

Cheers,

Marko
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Re: [gmx-users] PBC issues with membrane-peptide simulation

[Abhi Acharya]

Sorry for that Mark.

Basically, our experimental studies show that our designed peptides (2-3
different peptides)  are involved in membrane destabilization but their
activity (in terms of MIC values) varies. We want to understand the
molecular underpinnings of the membrane destabilization process and
possibly explain the variation in activities of the peptides. Therefore, we
wanted to perform some simulations starting from the point where some
amount of peptides are randomly added to the simulation box on one side of
the membrane (about 5 nm away from the upper leaflet) and see how the
system evolves.

The problem is that some of the peptides diffuse along the z-direction such
that they exit the simulation box and appear on the other side near to the
lower leaflet.

Hope this is helpful.

Thanks and Regards,
Abhishek Acharya





On Thu, Nov 10, 2016 at 9:57 AM, Mark Abraham 
wrote:

> Hi,
>
> You haven't said what you're trying to model, so it's going to be hard for
> someone to help out :-)
>
> Mark
>
> On Thu, 10 Nov 2016 05:21 Abhi Acharya  wrote:
>
> > Thank you Stephane for your suggestion. Though this seems like a nice
> > solution to circumvent the problem, but do you think this is the normal
> way
> > to go about it? I have never found anyone reporting such a methodology
> for
> > membrane peptide simulation. Also, I can anticipate significant increase
> in
> > computational costs for a double bilayer system. I have a 800 lipid
> > molecules in a single bilayer, so this is significant factor for me.
> >
> > Thanks and Regards,
> > Abhishek
> >
> > On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 <
> stephane.a...@cea.fr
> > >
> > wrote:
> >
> > > Hi,
> > >
> > > it is not an issue !! To resolve your problem you could simulate two
> > > bilayer in box and  insert the peptides between them.
> > >
> > > HTH
> > >
> > > --
> > >
> > > Message: 6
> > > Date: Wed, 9 Nov 2016 16:07:26 +0530
> > > From: Abhi Acharya 
> > > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation
> > > Message-ID:
> > >  > > gmail.com>
> > > Content-Type: text/plain; charset=UTF-8
> > >
> > > Dear Gromacs users,
> > >
> > > I am trying to simulate a system consisting of a lipid bilayer and few
> > > peptides. The peptides have been added randomly to the simulation box
> > only
> > > on one side of the membrane. I ran a 100 ns simulation of the system
> > using
> > > CHARMM36 forcefeild. However, I find that within the first few ns, some
> > of
> > > the peptides appear on the other side of the membrane. I think that
> this
> > is
> > > because of the diffusion of the peptides though the periodic boundary.
> > > Kindly suggest  how to tackle this problem. I have used COM motion
> > removal
> > > on the whole system for the said simulation.
> > >
> > > Regards,
> > > Abhishek Acharya
> > >
> > >
> > > --
> > >
> > > --
> > > Gromacs Users mailing list
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > > End of gromacs.org_gmx-users Digest, Vol 151, Issue 32
> > > **
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[gmx-users] doubt in PCA?

[Seera Suryanarayana]

Dear gromacs users,
I just want calculate the free energy difference between two
successive trajectories. As I know first we have to generate
contrivance matrices by using gmx covar and then have to execute the
gmx anaeig for eigenvector analysis. Here my doubt is how to give my
interest of trajectories? Suppose I want to have the free energy
difference between conformational sub state at 29800ps  and
conformational substate at 29900ps trajectory. How do I select these
two substaes in gmx covar and gmx anaeig? Kindly help me in this
regard.

Thanks in advance
Surya
Graduate student
India.
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Re: [gmx-users] compiling GROMACS with CUDA shared Libraries

[Mark Abraham]

Hi,

This will just happen by default, particularly if cmake can't find a static
library.

But you will likely find that actually running on a remote GPU will be
disastrous for performance. GROMACS is engineered around making use of
locality and both the CPU and GPU, in contrast with many of the targets for
things like rCUDA.

Mark

On Thu, 10 Nov 2016 04:40 Rizki Bayu  wrote:

> i currently using GROMACS to test a rCUDA server instance on my laboratory.
> It specified that any programs using rCUDA must be compiled with CUDA
> shared library by specifying it during the compilation (-cudart=shared on
> NVCC, -lcudart on GCC/++). Where do i have to put those option for GROMACS
> compilation?
>
> Thank you.
> Rizki Bayu
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Re: [gmx-users] PBC issues with membrane-peptide simulation

[Mark Abraham]

Hi,

You haven't said what you're trying to model, so it's going to be hard for
someone to help out :-)

Mark

On Thu, 10 Nov 2016 05:21 Abhi Acharya  wrote:

> Thank you Stephane for your suggestion. Though this seems like a nice
> solution to circumvent the problem, but do you think this is the normal way
> to go about it? I have never found anyone reporting such a methodology for
> membrane peptide simulation. Also, I can anticipate significant increase in
> computational costs for a double bilayer system. I have a 800 lipid
> molecules in a single bilayer, so this is significant factor for me.
>
> Thanks and Regards,
> Abhishek
>
> On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950  >
> wrote:
>
> > Hi,
> >
> > it is not an issue !! To resolve your problem you could simulate two
> > bilayer in box and  insert the peptides between them.
> >
> > HTH
> >
> > --
> >
> > Message: 6
> > Date: Wed, 9 Nov 2016 16:07:26 +0530
> > From: Abhi Acharya 
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation
> > Message-ID:
> >  > gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear Gromacs users,
> >
> > I am trying to simulate a system consisting of a lipid bilayer and few
> > peptides. The peptides have been added randomly to the simulation box
> only
> > on one side of the membrane. I ran a 100 ns simulation of the system
> using
> > CHARMM36 forcefeild. However, I find that within the first few ns, some
> of
> > the peptides appear on the other side of the membrane. I think that this
> is
> > because of the diffusion of the peptides though the periodic boundary.
> > Kindly suggest  how to tackle this problem. I have used COM motion
> removal
> > on the whole system for the said simulation.
> >
> > Regards,
> > Abhishek Acharya
> >
> >
> > --
> >
> > --
> > Gromacs Users mailing list
> >
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> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> > End of gromacs.org_gmx-users Digest, Vol 151, Issue 32
> > **
> > --
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Re: [gmx-users] PBC issues with membrane-peptide simulation

[Abhi Acharya]

Thank you Stephane for your suggestion. Though this seems like a nice
solution to circumvent the problem, but do you think this is the normal way
to go about it? I have never found anyone reporting such a methodology for
membrane peptide simulation. Also, I can anticipate significant increase in
computational costs for a double bilayer system. I have a 800 lipid
molecules in a single bilayer, so this is significant factor for me.

Thanks and Regards,
Abhishek

On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 
wrote:

> Hi,
>
> it is not an issue !! To resolve your problem you could simulate two
> bilayer in box and  insert the peptides between them.
>
> HTH
>
> --
>
> Message: 6
> Date: Wed, 9 Nov 2016 16:07:26 +0530
> From: Abhi Acharya 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs users,
>
> I am trying to simulate a system consisting of a lipid bilayer and few
> peptides. The peptides have been added randomly to the simulation box only
> on one side of the membrane. I ran a 100 ns simulation of the system using
> CHARMM36 forcefeild. However, I find that within the first few ns, some of
> the peptides appear on the other side of the membrane. I think that this is
> because of the diffusion of the peptides though the periodic boundary.
> Kindly suggest  how to tackle this problem. I have used COM motion removal
> on the whole system for the said simulation.
>
> Regards,
> Abhishek Acharya
>
>
> --
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>
> End of gromacs.org_gmx-users Digest, Vol 151, Issue 32
> **
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[gmx-users] gangle function to calculate the angle of the vector with the x and y axes

[Yan Shen]

Dear gromacs users,

I would like to calculate the angle between vector and x/y axes. When I
search the website there is a post about for gangle function add option to
calculate the angle of the vector with x/y axes. (see
https://redmine.gromacs.org/issues/1619 ) And in the post the target
version for this feature is 5.1. However, when I looked up gromacs versions
after 5.1, even in the latest gromacs manual there is still no option for
x/y axes (http://manual.gromacs.org/programs/gmx-gangle.html). I'm
wondering if I misunderstood the fix for this feature or is there any
particular version that has implemented this function.

Thanks,
Yan Shen
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[gmx-users] compiling GROMACS with CUDA shared Libraries

[Rizki Bayu]

i currently using GROMACS to test a rCUDA server instance on my laboratory.
It specified that any programs using rCUDA must be compiled with CUDA
shared library by specifying it during the compilation (-cudart=shared on
NVCC, -lcudart on GCC/++). Where do i have to put those option for GROMACS
compilation?

Thank you.
Rizki Bayu
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Re: [gmx-users] Convergence

[Billy Williams-Noonan]

Hey Justin, out of interest, when the PMF flattens at the end (the rate of
change is zero), how do we know that the PMF has truly converged?  Is there
some mathematical tool that can tell you the likelihood that the entire
conformational space has been sampled adequately?

On 10 November 2016 at 13:44, Justin Lemkul  wrote:

>
>
> On 11/9/16 2:54 PM, m g wrote:
>
>> Dear Justin Lemkul,You said "The PMF itself (being the primary output of
>> umbrella sampling) is a good start." for checking the convergence. what did
>> you mean? I was obtained PMF, did you mean that we check the overlap of
>> histogram of configurations?
>>
>
> Ask yourself: how would you check convergence of any quantity?  What does
> "convergence" mean?
>
> -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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-- 
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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Re: [gmx-users] Convergence

[Justin Lemkul]

On 11/9/16 2:54 PM, m g wrote:

Dear Justin Lemkul,You said "The PMF itself (being the primary output of umbrella 
sampling) is a good start." for checking the convergence. what did you mean? I was 
obtained PMF, did you mean that we check the overlap of histogram of configurations?


Ask yourself: how would you check convergence of any quantity?  What does 
"convergence" mean?


-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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[gmx-users] Convergence

[m g]

Dear Justin Lemkul,You said "The PMF itself (being the primary output of 
umbrella sampling) is a good start." for checking the convergence. what did you 
mean? I was obtained PMF, did you mean that we check the overlap of histogram 
of configurations? 
Many thanks
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[gmx-users] MPI on single quad-core

[Steve Seibold]

Hello 
I am attempting to run REMD on a single quad-core computer with gromacs 5 (MPI 
version). I was  hoping to run replicas on different threads...I was doing this 
to step up gromac scripts (make sure they run before I place them in the que!!) 
that I would then submit to a large "Advance Computing Center" running multiple 
nodes across multiple computers...
However, I have tried but have failed to get REMD to run on my one quad-core 
computer with Gromacs 5 mpi-version across many threads...Is this even possible?

If so, what are the commands to run it? I have tried "mpirun -np" and 
"mdrun_mpi -nt" etc...
Thanks, Steve
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[gmx-users] bootstrapping of PMF

[Alex]

Dear gromacs user,

I have performed a US simulation to find PMF of a peptide adsorbed to a
solid surface.

I have already evaluated the result by bootstrapping in gmx WHAM using the
b-hist method and 600 number of bootstraps and 1200 bins also with
considering the integrated autocorrelation time into account

Here is the command:

gmx wham -hist Histo.xvg -nBootstrap 600 -bins 1200 -bs-method b-hist
-bsres bsResult.xvg -bsprof bsProfs.xvg -if Fpull.dat -it TPR.dat -min 1.95
-max 4.7 -ac -o Profile.xvg -zprof0 4.69

And here are the result:

bsProfs.pdf
https://drive.google.com/open?id=0B_CbyhnbKqQDLWpnQzJ1WmlINXc

bsResult.pdf
https://drive.google.com/open?id=0B_CbyhnbKqQDRU5kRVdfaU5ObFE

iact.xvg   integrated autocorrelation time
https://drive.google.com/open?id=0B_CbyhnbKqQDOERHTXlrb095VUU

My first question is that if I have well converged PMF result, based on
above files?

I was also wondering that what exactly I have to be reported later in for
example a publication and ... ? the normal profile.xvg with out bootstrap
or this bsProfs.xvg? What is the difference between bsProfs.xvg and the
normal profile.xvg that we can get from normal gmx WHAM with out
bootstrapping?

And why the first 130 lines of iact.xvg file have been autocratically
commented out from  the rest?

And finally, do we always and here need to correct all the PMF profile by
the "$k_{B}T*log[4π(\epsilon)^2]$" factor in which \epsilon is reaction
coordinate? as been mentioned here:
Hub, J. S.; de Groot, B. L.; van der Spoel, D.J. Chem. Theory
Comput.2010,6, 3713-3720

Many thanks for your comments in advance.

Regards,
Alex
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Re: [gmx-users] Implicit solvent improvement in Gromacs 5.1.2

[Hai Nguyen]

On Tue, Nov 8, 2016 at 6:46 PM, Mark Abraham 
wrote:

> Hi,
>
> There's been no active work since 4.5 and no plans I've heard of. I hear
> AMBER is pretty good at it on GPUs :-)
>
>
Since Mark mentioned AMBER, just FYI for @Christian: AMBER have new and
more accurate model (GB-Neck2) too.

Hai


> Mark
>
> On Wed, Nov 9, 2016 at 12:04 AM Christian Bope Domilongo <
> christianb...@aims.ac.za> wrote:
>
> > Dear all,
> >
> > There is any improvement of GB implicit solvent in Gromacs package 5.1.2?
> >
> > Regards,
> > --
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Re: [gmx-users] Md simulation error

[Justin Lemkul]

On 11/8/16 2:07 PM, maria khan wrote:

Dear justin lemkul,,
Thanks alot..i like the way u answer my stupid questions..actually i dont
have anyone to guide me except u.thats why i ask even stupid questions.dont
mind please.i want to work under your supervision because i have passion
for simulation on gromacs.
Now coming to the point,,my problem was concerned with his residue of atom
HD1.I just went to pdb file and rename that HD1 to H3.then two files formed
that are  " "posre _protein chain_A.itp  and  topol_protein_chain _A.itp""
.while  topol.top   remained empty.now it gives me another error that is
" " Residue 'IS A' not found in residue topology database"".


http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

-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] sn-2 splitting

[Justin Lemkul]

On 11/8/16 2:48 PM, m g wrote:

Dear Justin Lemkul,In "kalp in dppc" tutorial, why can not see the splitting of 
the order parameter at the secondcarbon of sn-2 chain?Many thanks



The second carbon is present in the output; the terminal carbons (ester C and 
terminal methyl) cannot be computed because i-1 and i+1 vectors cannot be 
calculated.  Note that the output of gmx order starts with carbon 1 but this is 
actually carbon 2 in the chain (small output quirk).


-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] Adding hydrogen atom to specific Glu/Asp carboxyl oxygen atom

[Justin Lemkul]

On 11/9/16 7:07 AM, Dawid das wrote:

Yes, I have already figure that out, thanks ;). I have simply exchanged OE1
and OE2 atoms names and translated HE2 atom by vector between OE1 and OE2
in *gro file. Also I exchanged OE1 and OE2 atom names in *top file.



For future reference, simply switching the atom names and re-running pdb2gmx 
will save you all the manual work.


Note, too, that this is a rotatable bond so if, e.g. a hydrogen bond would be 
favorable, the carboxylic acid group will rotate to form that interaction, 
likely during a simple energy minimization.


-Justin


Best regards,
Dawid Grabarek

2016-11-09 12:56 GMT+01:00 Dd H :


Exchange their atom names？

Dading Huang

On Wed, Nov 9, 2016 at 7:23 PM, Dawid das  wrote:


Dear Gromacs Experts,

I know how to specify which Glu/Asp residues are to be
protonated/deprotonated with
pdb2gmx tool. However, I do not like that the hydrogen is added to one of
the oxygen atoms
of carboxyl moiety. I would like it to be found on the other oxygen. Is
there any other way
except modifying the *top file by hand?

Best regards,
Dawid
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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

==
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Re: [gmx-users] Adding hydrogen atom to specific Glu/Asp carboxyl oxygen atom

[Dawid das]

Yes, I have already figure that out, thanks ;). I have simply exchanged OE1
and OE2 atoms names and translated HE2 atom by vector between OE1 and OE2
in *gro file. Also I exchanged OE1 and OE2 atom names in *top file.

Best regards,
Dawid Grabarek

2016-11-09 12:56 GMT+01:00 Dd H :

> Exchange their atom names？
>
> Dading Huang
>
> On Wed, Nov 9, 2016 at 7:23 PM, Dawid das  wrote:
>
> > Dear Gromacs Experts,
> >
> > I know how to specify which Glu/Asp residues are to be
> > protonated/deprotonated with
> > pdb2gmx tool. However, I do not like that the hydrogen is added to one of
> > the oxygen atoms
> > of carboxyl moiety. I would like it to be found on the other oxygen. Is
> > there any other way
> > except modifying the *top file by hand?
> >
> > Best regards,
> > Dawid
> > --
> > Gromacs Users mailing list
> >
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Re: [gmx-users] Adding hydrogen atom to specific Glu/Asp carboxyl oxygen atom

[Dd H]

Exchange their atom names？

Dading Huang

On Wed, Nov 9, 2016 at 7:23 PM, Dawid das  wrote:

> Dear Gromacs Experts,
>
> I know how to specify which Glu/Asp residues are to be
> protonated/deprotonated with
> pdb2gmx tool. However, I do not like that the hydrogen is added to one of
> the oxygen atoms
> of carboxyl moiety. I would like it to be found on the other oxygen. Is
> there any other way
> except modifying the *top file by hand?
>
> Best regards,
> Dawid
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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[gmx-users] PBC issues with membrane-peptide simulation

[ABEL Stephane 175950]

Hi, 

it is not an issue !! To resolve your problem you could simulate two bilayer in 
box and  insert the peptides between them. 

HTH

--

Message: 6
Date: Wed, 9 Nov 2016 16:07:26 +0530
From: Abhi Acharya 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation
Message-ID:

Content-Type: text/plain; charset=UTF-8

Dear Gromacs users,

I am trying to simulate a system consisting of a lipid bilayer and few
peptides. The peptides have been added randomly to the simulation box only
on one side of the membrane. I ran a 100 ns simulation of the system using
CHARMM36 forcefeild. However, I find that within the first few ns, some of
the peptides appear on the other side of the membrane. I think that this is
because of the diffusion of the peptides though the periodic boundary.
Kindly suggest  how to tackle this problem. I have used COM motion removal
on the whole system for the said simulation.

Regards,
Abhishek Acharya


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End of gromacs.org_gmx-users Digest, Vol 151, Issue 32
**
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[gmx-users] Adding hydrogen atom to specific Glu/Asp carboxyl oxygen atom

[Dawid das]

Dear Gromacs Experts,

I know how to specify which Glu/Asp residues are to be
protonated/deprotonated with
pdb2gmx tool. However, I do not like that the hydrogen is added to one of
the oxygen atoms
of carboxyl moiety. I would like it to be found on the other oxygen. Is
there any other way
except modifying the *top file by hand?

Best regards,
Dawid
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[gmx-users] Fwd: PBC issues with membrane-peptide simulation

[Abhi Acharya]

Dear Gromacs users,

I am trying to simulate a system consisting of a lipid bilayer and few
peptides. The peptides have been added randomly to the simulation box only
on one side of the membrane. I ran a 100 ns simulation of the system using
CHARMM36 forcefeild. However, I find that within the first few ns, some of
the peptides appear on the other side of the membrane. I think that this is
because of the diffusion of the peptides though the periodic boundary.
Kindly suggest  how to tackle this problem. I have used COM motion removal
on the whole system for the said simulation.

Regards,
Abhishek Acharya
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