Dear all,
does anyone know if it is possible to somehow use COMPASS or CVFF
forcefields in Gromacs?
Thanks,
Andrei
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Hi Chris,
The two setups were different from each other in terms of only the number of
water molecules. Even the starting
conformations for the two peptides were the same. I especially took care
about that to leave only the number of molecules as a variable.
I calculated the error by dividing
I'm trying to repeat some X-ray diffraction analysis on lipid bilayers
according to the article:
http://dx.doi.org/10.1529/biophysj.104.046821 (it's free)
I have several corrected OPLS all-atom bilayer models and I need to
validate my model according to experimental x-ray diffraction data. But I
- Original Message -
From: Oleksandr nablaobl...@yahoo.com
Date: Wednesday, June 2, 2010 13:12
Subject: Re: [gmx-users] water clusters MD
To: Mark Abraham mark.abra...@anu.edu.au
There is some inconsistency between the top/itp files that
you provided.
The grompp gives an error Found
On Jun 2, 2010, at 9:49 AM, Ozge Engin wrote:
Hi Chris,
The two setups were different from each other in terms of only the
number of water molecules. Even the starting
conformations for the two peptides were the same. I especially took
care about that to leave only the number of molecules
- Original Message -
From: xho...@sohu.com
Date: Wednesday, June 2, 2010 14:17
Subject: Re: Re: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI error,
…..” occurs when using the ‘particle decomposition’ option.
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi, Mark,
Ok, thanks for the comments! I
think I will conduct the simulation withnbsp;‘constraints=hbonds’, since I had
done so in NAMD. I guess it wouldn't bring big
problem to the trajectory except increasing the compute cost.o:p/o:p -
Original Message -From: xho...@sohu.comdate: Wednesday, June
In addition to Marks e-mail and in order to close the topic I suggest you to
exempt people from your mentor comments in future.
O.
--- On Wed, 6/2/10, Mark Abraham mark.abra...@anu.edu.au wrote:
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] water clusters MD
To:
Hi all,
is there a way to get the hessian matrix for each time step
for which I also print out the trr? Or do I have to run
normal mode analysis for each configuration?
Thanks a lot
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gmx-users mailing listgmx-users@gromacs.org
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Please
Andrei Neamtu wrote:
Dear all,
does anyone know if it is possible to somehow use COMPASS or CVFF
forcefields in Gromacs?
You can probably implement just about anything by creating the right files
(.itp, nb.itp, bon.itp, .rtp, etc). Quite a bit of work, but not too
conceptually
Justin, thank you.
In fact I am worried about the cross coupling terms which apper i the
functional form of COMPASS and CVFF.
As far as I know in GROMACS there are no such terms, so I am asking if
there might be a solution to include these by editing .itp, nb.itp,
bon.itp, .rtp, etc, without the
Andrei Neamtu wrote:
Justin, thank you.
In fact I am worried about the cross coupling terms which apper i the
functional form of COMPASS and CVFF.
As far as I know in GROMACS there are no such terms, so I am asking if
there might be a solution to include these by editing .itp, nb.itp,
On 6/2/10 2:40 PM, Justin A. Lemkul wrote:
Andrei Neamtu wrote:
Justin, thank you.
In fact I am worried about the cross coupling terms which apper i the
functional form of COMPASS and CVFF.
As far as I know in GROMACS there are no such terms, so I am asking if
there might be a solution to
Dear All,
Before I start, I have already searched through the mailing list archives,
etc...and have energy minimized my structure (s) ;
I get the range check error;
_
Range checking error:
Explanation: During
On 02.06.2010, at 09:37, comc...@erg.biophys.msu.ru wrote:
I'm trying to repeat some X-ray diffraction analysis on lipid bilayers
according to the article:
http://dx.doi.org/10.1529/biophysj.104.046821 (it's free)
I have several corrected OPLS all-atom bilayer models and I need to
Dear all,
by doing MD simulations of a protein complex embedded in 2 membranes
(inner and outer membrane of bacteria, POPE), we observe a bilayer
splitting in one of the membranes. This has the effect that the bilayer
forms bubbles with vacuum inside.
It might have something to do with the PME
lloyd riggs wrote:
Dear All,
Before I start, I have already searched through the mailing list archives,
etc...and have energy minimized my structure (s) ;
I get the range check error;
_
Range checking error:
Hi,
I am trying to reproduce some steps from a paper, the authors set position
restraint to the protein (all-bonds) with a force constant of 1000 for 2ns.
I edited the pr.md file where nsteps would result in 2 ns, and I searched the
mailing list and knew that the force cons is 1000 by default
Thomas Schmidt wrote:
Dear all,
by doing MD simulations of a protein complex embedded in 2 membranes
(inner and outer membrane of bacteria, POPE), we observe a bilayer
splitting in one of the membranes. This has the effect that the bilayer
forms bubbles with vacuum inside.
We have seen
Rabab Toubar wrote:
Hi,
I am trying to reproduce some steps from a paper, the authors set
position restraint to the protein (all-bonds) with a force constant of
1000 for 2ns.
Constraints and restraints are different things in Gromacs, so setting position
restraints is done independently
Dear users
I have a dimer protein in the water box. It was run for 30ns.
during the simulation dimer split to two monomer. This things happen bc of
PBC. ( I checked it by vmd pbc option )
to have a two monomer together during trajectories (for visualization)
I have used the following command:
On 02/06/10 18:48, Morteza Khabiri wrote:
Dear users
I have a dimer protein in the water box. It was run for 30ns.
during the simulation dimer split to two monomer. This things happen bc of
PBC. ( I checked it by vmd pbc option )
to have a two monomer together during trajectories (for
On 02.06.2010, at 09:37, comc...@erg.biophys.msu.ru wrote:
I'm trying to repeat some X-ray diffraction analysis on lipid bilayers
according to the article:
http://dx.doi.org/10.1529/biophysj.104.046821 (it's free)
I have several corrected OPLS all-atom bilayer models and I need to
Hi, all,
I need to keep a molecule absolutely flat. I know about improper
dihedrals (i.e. gi_1), but it doesn't seem to be enough to keep it
flat. It seems to get bent a little bit. I have a system with a
phenyl ring and protons and I am trying to run GROMOS 96 ff53a6 force
field. I
Hi Tom,
Thanks for your replay. From the paper (DNA and lipid bilayers:
self-assembly and insertion. J. Royal Soc. Int. 5, S241-S250, 2008. ) I
understand that the DNA CG particles where identical to the one used for
lipids and protein, am I correct? Also, they had used elastic network to
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