Shuangxing Dai wrote:
Hi, all,
I was wondering if the shell molecular dynamics exclude the
electrostatic interaction automatically. According to the shell model,
the interaction between core and shell in replaced by the harmonic
interaction. If not, how to exclude electrostatic in
Dear List,
I m trying to run an NPT simulation at 600K which looks unrealistic. I m
running minimization followed by anealing and then NPT simulation (mdp files
are attached). The job keeps running but after 162 ps, the CPU usage
gradually decreases to 26% without any further output. Your help is
Hi, all,
I was wondering if the shell molecular dynamics exclude the
electrostatic interaction automatically. According to the shell model, the
interaction between core and shell in replaced by the harmonic interaction.
If not, how to exclude electrostatic interaction between them?
trjconv
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hamme
Hi Tsjerk,
I looked at the .trr file and cannot read this file and simply delete
lines to create a sub-trajectory. So, how do I create a sub-trajectory
to analyze?
Thanks.
Darrell
Date: Wed, 25 Nov 2009 09:04:01 +0100 From: Tsjerk Wassenaar
Subject: Re: [gmx-users] Unexpected behavior of
I have a further question about tabulated non-bonded potentials.
The manual (6.7.2) says:
"It is also possible to combine a standard Coulomb with a modified LJ
potential... The table file must always contain the 7 columns however,
and meaningful data (i.e. not zeroes) must be entered in all column
Hi,
> Removing periodicity from the trajectory can be done after simulation
> using g_traj with the "-nojump" option.
Actually,
trjconv -pbc nojump
Cheers,
Tsjerk
>
> Best,
> Lukasz
>
> --
> Lukasz Cwiklik
> http://cwiklik.wordpress.com
> --
> gmx-users mailing list gmx-us...@gromacs.org
>
Please choose an informative subject line, as it will help attract the attention
of someone interested in helping you.
PAVAN RELISH DESTINY RESOLVING CRUX OF LIFE. wrote:
I am new to Gromacs & using it with Amber force field amber03,
i am able 2 run my system
On Tue, Nov 24, 2009 at 1:09 PM, Omer Markovitch wrote:
> On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin wrote:
>>
>> So, how can I remove the periodic boundary condition to get the truly
>> movement of the atoms between the two time steps ?
>
> Removing PBC and placing atoms back into their "true"
Dear all,
We are experimenting with mdrun-openmm on a high end Nvidia Type graphics card
and CUDA attached to the local NGS cluster computer. The simulation for smaller
systems runs fine, but when one moves to bigger files it turns out that all the
result files (xtc, pdb edr and log) are stored
That info is in the GROMACS manual - a very nice manual with lots of effort put
in to answer such questions.
A.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of subarna thakur [thakur.suba...@yahoo.co.in]
Sent: 25 November
Hi
Can any body please tell me what does c0 and c1 column represent in .itp file?
And how do I obtain these parameters for a ligand.
Subarna thakur
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gmx-users mailing listgmx-users@gromacs.org
Hi:
In my hands, the command
editconf -f input.gro -o output.gro
does not follow the PDB rules as regards the residue name. W from the
.gro file (obtained by
genconf -f water.gro -nbox 2.5 2.5 2.0 -0 out.2.5.2.5.2.0.gro)
where water.gro is from MARTINI web page, is placed correctly as atom
(co
Hi Darrell,
You can check whether the output is identical to a trajectory of the
specified frames...
It may well be that the counting for the regression is done on the frames read:
100 - 60 = 40 ps
Then 4 and 35.9 would correspond to 64 and 95.9. The answer is in the
code... But using a subtrajec
I am new to Gromacs & using it with Amber force field amber03,
i am able 2 run my system of DNA till steepest descent but when
i tried to run it for cg it showed
that can not work with so much of constrains so i tried to run
it with -Dposres
dire
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