On 1/19/13 5:21 PM, Mehdi Bagherpour wrote:
hello everybody
I have simulated DNA using CHARMM force field for 50 ns with 2 ps snapshots
for each step.
when I wanted to convert .xtc trajectory files to .pdb using trjconv, some
of the snapshots were collaborated.
I have used periodic boundary c
On 1/19/13 4:57 PM, Mortuza Munna wrote:
Thank you Justin and Rajat. It is a very helpful information for me indeed. It
seems, I have to write an awk/sed/bash script to rotate each split frame, as I
will have at least 3000 frames after splitting. Moreover, I have 30 simulations
like this. Howev
hello everybody
I have simulated DNA using CHARMM force field for 50 ns with 2 ps snapshots
for each step.
when I wanted to convert .xtc trajectory files to .pdb using trjconv, some
of the snapshots were collaborated.
I have used periodic boundary conditions in this simulations.
To convert, I use
On 1/18/13 7:09 PM, Mortuza Munna wrote:
Dear gromacs user,
I have found that g_bundle can measure the angle between a group from
index file and z-axis with the option -z. Is it possible to measure the angle
of that group from index file with y-axis/x-axis? Any suggestion will be
appreciable.
Dear All,
I made a qm/mm implementation using gromacs as mm part.
Qm part can be in principle any qm method (now only FHI-aims implemented).
There can be more than one QM regions.
Documentation:
https://wiki.fysik.dtu.dk/ase/ase/calculators/ase_qmmm_manyqm.html#module-ase_qmmm_manyqm
terveisin,
On 1/19/13 10:46 AM, fatemeh ramezani wrote:
Dr. Justin
In GOLP paper is written: Water molecules were kept rigid with the SETTLE
algorithm,
but in its commented md.mdp file is written
define =
;GOLP has been tested with lincs only
constraint = none
constraint_algorithm =
Dr. Justin
In GOLP paper is written: Water molecules were kept rigid with the SETTLE
algorithm,
but in its commented md.mdp file is written
define =
;GOLP has been tested with lincs only
constraint = none
constraint_algorithm = lincs
according to manual, SETTLE can be s
Dear Justin,
Thank you very much from your help.
Best Regards
Dina
- Original Message -
From: Justin Lemkul
To: dina dusti ; Discussion list for GROMACS users
Cc:
Sent: Saturday, January 19, 2013 3:16 PM
Subject: Re: [gmx-users] concatenate of .edr files
On 1/19/13 5:48 AM, din
Why don't you try rotating your simulation box using editconf (.gro) or
trjconv (.xtc)
On Sat, Jan 19, 2013 at 5:39 AM, Mortuza Munna wrote:
> Dear gromacs user,
> I have found that g_bundle can measure the angle between a group from
> index file and z-axis with the option -z. Is it possible to
I have questions about your work:
1-I see previous your posts , do you have equlibrium structure of gold
nanoparticle?
2- about nanoparticle, gold atoms at surface have difference behaviour of
internal atom?? do you idea about it?
3- you include interation of "Au" only with "S" according to Gul
On 1/19/13 7:11 AM, fatemeh ramezani wrote:
Dr. Justin
I want to do energy minimization of AU and Protein in separate steps and in
last emails you said a way for this, is freezing of them. Then I decide to
freeze AU and minimize Protein and in next step vise versa. I'm wrong?
You can cert
Dr. Justin
I want to do energy minimization of AU and Protein in separate steps and in
last emails you said a way for this, is freezing of them. Then I decide to
freeze AU and minimize Protein and in next step vise versa. I'm wrong?
Fatemeh Ramezani
--
gmx-users mailing listgmx-users@groma
On 1/19/13 5:48 AM, dina dusti wrote:
Dear GROMACS Users,
I have simulations with 120 ps and the file names are md.*, then I expended
the time of simulation to 240 ps, with file names next as are follow:
tpbconv -s md.tpr -extend 120 -o next.tpr
mdrun -v -deffnm next -s next.tpr
Dear GROMACS Users,
I have simulations with 120 ps and the file names are md.*, then I expended
the time of simulation to 240 ps, with file names next as are follow:
tpbconv -s md.tpr -extend 120 -o next.tpr
mdrun -v -deffnm next -s next.tpr -cpi md.cpt
I use from trjcat to concaten
Dear Developers!
Today in the download section on gromacs web I've found 2 new verions
of gromacs ( 4.6 and 4.5.6) aviable for downloading. Does it final
releases and in what they differs?Have both of them native GPU
support ?
James
2013/1/17 James Starlight :
> Thank you!
>
> It's a good news
The paper looks good. Do some more work and publish many
Sent from my iPhone
On 17-Jan-2013, at 8:18 PM, "James Starlight" wrote:
Dear Gromacs Developers!
Using sd1 integrator I've obtain good performance with the core-5 +
GTX 670 ( 13ns\per day) for the system of 60k atoms. That results on
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