On 7/31/14, 1:16 AM, Meenakshi Rajput wrote:
hi gromacs users
I have done the whole mdrun simulation of my protein human serum albumin
complex with ligand and i got all the files. But when i opened the pdb file
obtained after md simulation in pymol to see the interaction, ligand went
to some
How should I correct the input file?
Urszula Uciechowska
On 7/31/14, 7:42 AM, Urszula Uciechowska wrote:
Dear Gromacs users,
I tried to run coarse grained MD however after a few steps I got:
Step 39, time 0.78 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.038933,
On 7/31/14, 8:16 AM, Urszula Uciechowska wrote:
How should I correct the input file?
http://manual.gromacs.org/online/mdp_opt.html#vel
And get your hands on some suitable tutorial material; proper use of these
settings is routine.
-Justin
Urszula Uciechowska
On 7/31/14, 7:42 AM,
Can anyone help me with this error file? I did not get the log file...
Back Off! I just backed up md.log to ./#md.log.5#
Reading file md10ns-2.tpr, VERSION 4.5.3 (single precision)
Reading checkpoint file md10ns.cpt generated: Mon Jul 21 20:45:14 2014
Gromacs binary or parallel settings not
I have changed the Pcoupl into parrinello-rahman and I have still the same
error. The input file was taken from the martini webpage
http://md.chem.rug.nl/cgmartini/index.php/proteins
define = -DPOSRES
dt = 0.02
nsteps = 25000
nstxout = 0
nstvout
Dear Justin,
I'm in the experimenting with [exclusions] for [thole_polarization].
Still not there but approaching... I'd like to ask more help as the
Manual is not detailed enough for me to comprehend the whole.
When using the core/shell model I expect the following extra
effects and functions
On 7/31/14, 8:36 AM, Urszula Uciechowska wrote:
Can anyone help me with this error file? I did not get the log file...
There is no error here. I assume this is what is concerning:
Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not
On 7/31/14, 8:41 AM, Urszula Uciechowska wrote:
I have changed the Pcoupl into parrinello-rahman and I have still the same
error. The input file was taken from the martini webpage
http://md.chem.rug.nl/cgmartini/index.php/proteins
From my experience, the settings in the equilibration.mdp
Hi,
On Tue, Jul 29, 2014 at 6:18 AM, Cara Kreck cara_...@hotmail.com wrote:
Is it possible to use a position variable in conjunction with x,y,z
keywords in g_select?
Unfortunately, this is currently not possible.
I'm trying to select all molecules within a channel embedded in a membrane.
Dear Justin,
1. With a q_D charge on D, the normal q_A becomes q_C=q_A-q_D
to preserve the q_A=q_C+q_D atomic charge in a c/s simulation
(since D is attached to A). I assume that GROMPP expects q_C for
atoms, q_D for shell particles in the GRO files. Is this correct?
No. Every atom in
On 7/31/14, 2:17 PM, Tamas Karpati wrote:
Dear Justin,
1. With a q_D charge on D, the normal q_A becomes q_C=q_A-q_D
to preserve the q_A=q_C+q_D atomic charge in a c/s simulation
(since D is attached to A). I assume that GROMPP expects q_C for
atoms, q_D for shell particles in the GRO
On 7/31/14, 10:51 PM, Andy Chao wrote:
Dear GROMACS Users:
I tried to use the g_tcaf command to calculate the viscosity of the ionic
liquid. I got the following error message while using the following
command:
g_tcaf -f NPT.trr -s NPT.tpr -n index.ndx -o tcaf.xvg
The error message is the
Teemu,
I suspected that might have been the case. It would be good to see a z of
option in a future version, if you find the time.
Thanks,
Cara
Date: Thu, 31 Jul 2014 20:47:11 +0300
From: teemu.murt...@gmail.com
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] g_select position
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