On 27/02/2012 5:03 PM, James Starlight wrote:
Justin,
2012/2/25 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
You likely have a [settles] directive applied the the XW molecules
(crystal waters, yes?) and SOL. You can't do that. The block of
molecules to which
On 27/02/2012 6:35 PM, zhongjin wrote:
Dear GMX users,
I find that tau_p value is very important to NTP simulation, when I
use tau_p = 1ps, the default value, the box change a lot, only when I
use tau_p = 10 ps, it is OK.
; Pressure coupling
Pcoupl = Parrinello-Rahman
Mark,
I've found a possible sollution to restrict oxygens of my X-ray water by
possible plasing the below string in the TOPOLOGY.top of my system
; Include X-ray water topology
#include XW.itp
; Include Position restraint file
#ifdef POSRES_XW
[ position_restraints ]
; i funct fcx
On 27/02/2012 8:35 PM, James Starlight wrote:
Mark,
I've found a possible sollution to restrict oxygens of my X-ray water
by possible plasing the below string in the TOPOLOGY.top of my system
; Include X-ray water topology
#include XW.itp
; Include Position restraint file
#ifdef POSRES_XW
[
The ionic liquid is bistriflate N-methyl-N-propyl pyrrolidinium and the
force field is from Lopes (CLaP). I tried deleting all of the cation
dihedrals from the itp file and found that the run did not crash, although
it still had a positive coul recip term. Upon examination of the cation
Dear Justin and All
Right now, I am trying to add new residue in OPLS-aa ff
when I make the following grompp -f file.mdp -c file.gro -p file.top -o file
I have the following error
Program grompp, VERSION 4.5.2
Source code file: toppush.c, line: 1071
Fatal
Dear Justin and All
Right now, I am trying to add new residue in OPLS-aa ff
when I make the following grompp -f file.mdp -c file.gro -p file.top -o file
I have the following error
Program grompp, VERSION 4.5.2
Source code file: toppush.c, line: 1071
priya thiyagarajan wrote:
hello sir,
Thanks for your kind reply..
i tried like what you suggest..
i used the command
mdrun -s md60.tpr -cpi state.cpt -o md60.trr -x traj.xtc -e md60.edr -c
md60.gro -g md60.log
to extend my simulation..
but again i got error as follows
Reading file
Good Day,
I ran a molecular dynamic simulation for over a month and I gathered the
.pdb file containing the molecular structure at the end of the
simulation. I can see the final configuration using a pdb viewer but I
would like to know if it is possible (without redoing the simulation) to
obtain
The trajectory file contains that information (.xtc or .trr).
You can do a couple of things here:
# load the trajectory using your viewer (be careful if the trajectory is large,
you may want to change the number of frames it contains using trjconv)
# extract the coordination files (.gro or .pdb)
Hi,
I have run a simulation of a fixed object in water using gromacs. Now, I want
to analyze only water molecules which are present within a cylinder of certain
radius (smaller than simulation box dimension in XY plane).
I wonder whether gromacs has any particular tool which can identify the
On 28/02/2012 10:49 AM, Sanku M wrote:
Hi,
I have run a simulation of a fixed object in water using gromacs.
Now, I want to analyze only water molecules which are present within a
cylinder of certain radius (smaller than simulation box dimension in
XY plane).
I wonder whether gromacs has
Maybe you can try trjorder to order the water molecules around your protein
and make a group of those nearest water molecules and output them using trjconv
Jianguo
From: Sanku M msank...@yahoo.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hello,
Is it possible to analyse structure during running simulation?
Hw we can do that
Thanks and Regards,
--
Vishwambhar
Centre for Bioinformatics
Pondicherry University
Pondicherry
--
Note: Strictly confidential to Vishwayogi
--
gmx-users
hello sir,
while performing simulation for 30ns, because of queue time limit my run
terminated at 11.6ns.. then i extended my simulation using mdrun as you
suggest..
while doing so i got error as
Fatal error:
Failed to lock: md20.log. Function not implemented.
For more information and tips for
On 28/02/2012 3:50 PM, priya thiyagarajan wrote:
hello sir,
while performing simulation for 30ns, because of queue time limit my
run terminated at 11.6ns.. then i extended my simulation using mdrun
as you suggest..
while doing so i got error as
Fatal error:
Failed to lock: md20.log.
On 28/02/2012 3:36 PM, Vishwambhar Bhandare wrote:
Hello,
Is it possible to analyse structure during running simulation?
Hw we can do that
Make a copy of the trajectory file and then do whatever you want.
Mark
--
gmx-users mailing listgmx-users@gromacs.org
Thanks. But Does that mean that I should look in pullf.xvg of each window
and see whether the value is converged or not. If not then I should extend
the simulation.
Shahid Nayeem
On Sat, Feb 25, 2012 at 12:05 AM, Justin A. Lemkul jalem...@vt.edu wrote:
shahid nayeem wrote:
My protein
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