Peter,
Thanks for advise.
I've found already pre-equilibrated POPC bilayers with 200 lipids. I've
examined that lipids and found that they are very similar to the berger's
lipids (it consists of equal nymber of atoms ) but the atom order in each
lipid is slightly different than in Tieleman's popc
Dear Group
If any of you guys have partial charges for the anilinium ion, please send me
a reply or pose it
thanks
Milinda Samaraweera
University of Connecticut
Department of Chemistry
55 N Eagleville road
unit 3060
Storrs CT
USA--
gmx-users mailing listgmx-users@gromacs.org
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On 5/27/12 8:44 PM, Justin A. Lemkul wrote:
On 5/27/12 8:41 PM, sai nitin wrote:
Dear all,
Recently i performed two 15ns simulation of protein-ligand systems using
gromacs of my interest...and using g_energy tool..i calculated crude
interaction energy based on short-‐range energy component
On 5/27/12 8:41 PM, sai nitin wrote:
Dear all,
Recently i performed two 15ns simulation of protein-ligand systems using
gromacs of my interest...and using g_energy tool..i calculated crude
interaction energy based on short-‐range energy components Eint = +
. ...I got two Eints for two simu
Dear all,
Recently i performed two 15ns simulation of protein-ligand systems using
gromacs of my interest...and using g_energy tool..i calculated crude
interaction energy based on short-‐range energy components Eint =
+ . ...I
got two Eints for two simulations
1) Eint = -51.003 Kcal/mol (firs
Greetings,
http://www.gromacs.org/Downloads/Installation_Instructions/GPUs?highlight=pe
riodicity#GPU_Benchmarks has benchmarks for the GTX 580. However, that card
is no longer state of the art. The GTX 690 has 6 times as many stream
processors, over twice the memory and a higher clock speed. O
On 28/05/2012 8:14 AM, Igor Druz wrote:
>/ You need to choose a large .xtc precision, or use nstxout and filter the
group
/>/ afterwards./
/
/
/I tried xtc-precision=100. This gives the same result as the default
value//xtc-precision=1000./
That seems highly unlikely. Can you demonstrat
>* You need to choose a large .xtc precision, or use nstxout and filter the
>group*>* afterwards.*
*
*
*I tried xtc-precision=100. This gives the same result as the
default value **xtc-precision=1000. Yet, the results are different
from the analysis of the trr file.*
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gmx-users mailing li
On 5/27/12 5:52 PM, Mark Abraham wrote:
On 28/05/2012 7:48 AM, Justin A. Lemkul wrote:
On 5/27/12 5:29 PM, Igor Druz wrote:
I would like to save disk space and write only protein coordinates using
xtc-grps, but preserve the same precision as in trr file. What value of
xtc-precision should
On 28/05/2012 7:48 AM, Justin A. Lemkul wrote:
On 5/27/12 5:29 PM, Igor Druz wrote:
I would like to save disk space and write only protein coordinates using
xtc-grps, but preserve the same precision as in trr file. What value of
xtc-precision should be used to achieve this?
Why not write a
On 5/27/12 5:29 PM, Igor Druz wrote:
I would like to save disk space and write only protein coordinates using
xtc-grps, but preserve the same precision as in trr file. What value of
xtc-precision should be used to achieve this?
Why not write a .trr file with the desired frequency? What you
On 5/27/12 5:26 PM, vijaya subramanian wrote:
Hi
Yes, I do have gromacs xtc files. I don't know how to use the .tpr files in
conjunction with .xtc files which don't have the whole system in them (all
atoms)
ie. if I have an xtc file without the solvent or an xtc file which is filtered
along on
I would like to save disk space and write only protein coordinates using
xtc-grps, but preserve the same precision as in trr file. What value of
xtc-precision should be used to achieve this?
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Plea
On 5/27/12 5:03 PM, vijaya subramanian wrote:
one conect record for all models?
You need the CONECT records for visualization, right? Or is there some other
purpose? In theory, if you have one .pdb file with CONECT records, you can load
your trajectory as data for it and the bonds should
one conect record for all models?
thanks-
Date: Sun, 27 May 2012 20:24:59 +0200
Subject: Re: [gmx-users] trjconv -conect
From: tsje...@gmail.com
To: jalem...@vt.edu; gmx-users@gromacs.org
CC:
Hi Vijaya,
Just copy the CONECT records from the reference pdb afterwards.
Cheers,
Tsjerk
On May 27, 20
On 5/27/12 4:58 PM, vijaya subramanian wrote:
So how do people use trjconv -conect? It says in the manual it is useful for cg
results-
Most Gromacs programs assume that you have Gromacs input files at your disposal.
A .tpr file is a simulation input file and thus is accessible to anyone wh
Hi Vijaya,
Just copy the CONECT records from the reference pdb afterwards.
Cheers,
Tsjerk
On May 27, 2012 7:42 PM, "Justin A. Lemkul" wrote:
On 5/27/12 1:36 PM, vijaya subramanian wrote:
> Hi
>
> > I don't have a .tpr file for the cg system. I am anlayzing results from
> pca and > the trajec
On 5/27/12 1:36 PM, vijaya subramanian wrote:
Hi
I don't have a .tpr file for the cg system. I am anlayzing results from pca and
the trajectories only have calpha atoms.
Can I generate a .tpr for just calpha?
Not without your own custom force field. No Gromacs force field is compatible
wi
Hi
I don't have a .tpr file for the cg system. I am anlayzing results from pca
and the trajectories only have calpha atoms.
Can I generate a .tpr for just calpha?
> Date: Sun, 27 May 2012 12:12:14 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] trjconv -c
On 5/27/12 12:05 PM, vijaya subramanian wrote:
Hi
I am trying to add conect records to a cg trajectory under gromacs 4.5.4 as
follows:
trjconv -s CONECT.PDB -f traj.xtc -conect -o testconect.pdb
or with one frame
trjconv -s CONECT.PDB -f oneframe.pdb -conect -o testconect.pdb
but dont see
Hi
I am trying to add conect records to a cg trajectory under gromacs 4.5.4 as
follows:
trjconv -s CONECT.PDB -f traj.xtc -conect -o testconect.pdb
or with one frame
trjconv -s CONECT.PDB -f oneframe.pdb -conect -o testconect.pdb
but dont see any conect records in the output file.
The cone
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