Hi GMX users:
I did a simulation of a bilayer, and I would like to calculate the diffusion
coefficent of lipids by g_msd command.
I used the following command:
g_msd -s *.tpr -f *.xtc -n index.ndx -beginfit xx -endfit xx -trestart xx -o
msd.xvg
I have 144 lipids in one leaflet. I am wondering w
Justin and Mark, many thanks for your help.
With regards to the parallelization, when did parallel membed become
supported? I¹ve just tried on 5.0.4 and I¹m getting the response:
Reading file membed_NPT_B.tpr, VERSION 5.0.4 (double precision)
-
Hello all,
I am trying to find viscosity using green kubo relation for Ionic Liquids.
I got pressure tensor values (pxx, pyy, pzz, ….) from energy file .edr. How
to get stress autocorrelation function (SACF) from pressure autocorrelation
function in MD simulations? Also how to change ACF windows
On Fri, 8 Jan 2016, Bin Liu wrote:
Hi Tsjerk,
I replicated their settings in their papers. The system size I used is
larger than what they had. Could you elaborate on the reference used for
fitting? Thank you so much.
About the importance of the reference structure used for fitting in
Cartes
On 1/8/16 12:35 PM, shagun krishna wrote:
Dear Justin,
Thanks a lot. I have successfully completed mdrun with -rerun option. I
have ran the mdrun command on the original mdrun.xtc using new .mdp
settings without PME, and the result was stored in new .edr file. This new
.edr file was then subje
Hi Tsjerk,
I replicated their settings in their papers. The system size I used is
larger than what they had. Could you elaborate on the reference used for
fitting? Thank you so much.
Cheers,
Bin
Message: 3
Date: Fri, 8 Jan 2016 18:29:26 +0100
From: Tsjerk Wassenaar
To: Discussion list for GROM
Dear Justin,
Thanks a lot. I have successfully completed mdrun with -rerun option. I
have ran the mdrun command on the original mdrun.xtc using new .mdp
settings without PME, and the result was stored in new .edr file. This new
.edr file was then subjected to g_energy to obtain the values of LJ-17
Hi Bin,
Did you use the same force field, simulation length, other parameters? The
system size might play a role too. And for trialanine the reference used
for fitting may matter too. But first check all the other
similarities/differences.
Cheers,
Tsjerk
On Jan 8, 2016 16:35, "Bin Liu" wrote:
Hi Tsjerk,
I used trjconv -pbc and trjconv -nojump to remove PBC and jump across the
boundary before I applied g_covar. This paper is about dPCA indeed. But it
also contains the author's results on cPCA. Thank you for your help.
Regards,
Bin
Message: 6
Date: Thu, 7 Jan 2016 23:38:44 +0100
Fr
Hi,
The current implementation of membed is quite sane and should support all
kinds of parallelization. (It is difficult to say much that is nice about
the first implementation, though!)
gmx trjconv and convert-tpr are good for making subsets from well chosen
index groups.
Mark
On Fri, 8 Jan 20
On 1/8/16 12:00 AM, Agnivo Gosai wrote:
Dear Users,
I use GROMACS to do SMD simulation. I have the pullf.xvg file , but it is
very large. I also have the smd.xtc file. I have used it to calculate the
COM separation distance between the two pulled groups.
I want to plot force vs COM separation
On 1/8/16 12:50 AM, shagun krishna wrote:
Hiii Justin,
Thank you very much for your help. After changing my settings according to
your suggestions I am not getting the previous errors. :) The grompp
command ran successfully, but when I am evoking the mdrun using rerun
option I am getting a fat
On 1/8/16 3:38 AM, Nash, Anthony wrote:
> Many thanks Justin, that’s solved it.
>
> The simulation is now running, reporting that 8 POPC molecules and 12 SOL
> molecules have been removed. However, I have a bit of a problem. I don’t
> seem to be able to get the -membed option working on a parall
On 1/8/16 5:46 AM, 张敏华 wrote:
Hi everyone, I encountered a problem when I using pdb2gmx to convert a pdb file
into gro and top file. The system give me a fatal error message as following:
Fatal error:
Residue 145 named LYS of a molecule in the input file was mapped
to an entry in the topology
http://selene.princeton.edu/FFPTM/
On Fri, Jan 8, 2016 at 9:52 AM, Simone Bolognini
wrote:
> Hi everyone,
> I need to run some MD simulations with a protein where a particular serine
> should be phosphorylated. Since in the original pdb the serine is actually
> not, I guess I should modify somet
Hi everyone, I encountered a problem when I using pdb2gmx to convert a pdb file
into gro and top file. The system give me a fatal error message as following:
Fatal error:
Residue 145 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used i
Hi everyone,
I need to run some MD simulations with a protein where a particular serine
should be phosphorylated. Since in the original pdb the serine is actually
not, I guess I should modify something 'by hand'. I'm going to use
AMBER-ILDN ff. Can anyone of you tell me what should I do? My first g
Many thanks Justin, that’s solved it.
The simulation is now running, reporting that 8 POPC molecules and 12 SOL
molecules have been removed. However, I have a bit of a problem. I don’t
seem to be able to get the -membed option working on a parallel
installation of gromacs, only serial. I assume pa
This was very useful thanks!! Actually I realized that Swiss Pdb Viewer
automatically tries to reconstruct the missing atom positions, so that now
I have the topology.
Thanks a lot!
Simone
Il giorno ven 8 gen 2016 alle ore 00:02 Peter Stern <
peter.st...@weizmann.ac.il> ha scritto:
> Look for an
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