Hello Chris,
Thank you very much for your reply. I have done following test as you suggested
to check whether the checkpoint file are corrupted.
1) Yes, I have used same version of gromacs for mdrun and to produce .cpt file.
2) when i do gmxcheck -f 0.cpt # i get the same error.
Please use an informative subject.
ITHAYARAJA wrote:
Dear Sir,
when i am doing energy minimization (grompp), i found following error
CMD : grompp -f em.mdp -c proteinGR_b4ion.gro -p proteinGR.top -o
proteinGR_b4ion.tpr
WARNING 1 [file em.mdp, line unknown]:
Unknown or double left-hand
Dear gmx-users,
I'm doing several simulations of a monomeric protein with different ligands.
I had several frustrating experiences because I found that at the end of
simulations, I found that my complexes violate the minimum periodic image
distance.
I'm using Gromacs 4.5.3 and for all my
Parul tew wrote:
Thanks for the reply Justin,
This is how I added the position restraint in topology
--
; Include DPPC chain topology
#include dppc.itp
#ifdef POSRES_LIPID
; Position restraint for each lipid
I am somewhat confused. When I do umbrella sampling, I use a bash
script to set up a number of separate restrained simulations. Thus I
would get one .cpt file for each simulation. What are you doing that
in addition to these .cpt files you also get a state.cpt and
state_perv.cpt? Perhaps
Anna Marabotti wrote:
Dear gmx-users,
I'm doing several simulations of a monomeric protein with different
ligands. I had several frustrating experiences because I found that at
the end of simulations, I found that my complexes violate the minimum
periodic image distance.
I'm using Gromacs
Hello Chris,
I followed the steps as mentioned in the umbrella sampling tutorial in gromacs.
After NPT equilibration step, i did the umbrella simulation runs. Below are the
commands which i used:
grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx -o
umbrella0.tpr
Poojari, Chetan wrote:
Hello Chris,
I followed the steps as mentioned in the umbrella sampling tutorial in gromacs.
After NPT equilibration step, i did the umbrella simulation runs. Below are the
commands which i used:
grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n
Justin A. Lemkul wrote:
Poojari, Chetan wrote:
Hello Chris,
I followed the steps as mentioned in the umbrella sampling tutorial in
gromacs.
After NPT equilibration step, i did the umbrella simulation runs.
Below are the commands which i used:
grompp -f md_umbrella.mdp -c npt0.gro -t
Hello Justin,
Thank you very much for your reply.
I must hav used -cpo 0.cpt instead of -o 0.cpt.
Kind Regards,
chetan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 20
Poojari, Chetan wrote:
Hello Justin,
Thank you very much for your reply.
I must hav used -cpo 0.cpt instead of -o 0.cpt.
Are you saying the commands shown below are wrong? Using -cpo 0.cpt is indeed
the correct approach.
-Justin
Kind Regards,
chetan
Hi Justin,
Except for cpt i think rest of the command should be alright.
For outputting cpt file and using it for extending runs, i must have used -cpo
and not -o flag.
Kind Regards,
chetan
From: gmx-users-boun...@gromacs.org
Dear justin,
Thank you fro your previous reply
when i run SMD using the same force ( same rate constant and same rate) in
different box having different dimension. will it affect the result of
simulation
I am asking the effect of box dimension on pull in group (keeping
vidhya sankar wrote:
Dear justin,
Thank you fro your previous reply
when i run SMD using the same force ( same rate constant and same rate)
in different box having different dimension. will it affect the result
of simulation
I am asking the effect of box dimension on
Dear gmx-users,
I am trying to perform the Normal Mode Analysis of 24 kDa protein in water.
Here is the .mdp file I am using:
integrator = nm
dt = 0.002
nsteps = 1
emtol = 1
nstcomm = 1
nstxout = 0
nstxtcout
On 21/09/2011 1:38 AM, Andrey Dyachenko wrote:
Dear gmx-users,
I am trying to perform the Normal Mode Analysis of 24 kDa protein in
water. Here is the .mdp file I am using:
integrator = nm
dt = 0.002
nsteps = 1
emtol = 1
nstcomm
Dear justin thank for your previous reply
I have Adjusted My box vectors along only one pulling dimension.
I am pullling for distance of 5 nm from the center of box along Z axis i am
using the following option in editconf_d my command is as follows
./editconf_d -f protein.gro -o
Hi
I have a geometry in a textfile which looks like that:
N 2.823790 -0.041893 0.737832
C 3.563329 -1.141307 0.332899
O 4.781032 -1.165954 0.346660
You see the atom and then three spatial coordinates. I renamed it to
Hi,
I'd like to perform TI calculations as described in section 3.12.2 of the
(version 4.5.4) manual.
my questions are:
1) i understand in Gromacs TI/FEP is implemented as a single topology, and not
dual topolgy
algorithm, is that correct?
2) to successfully analyze the results with BAR
vidhya sankar wrote:
Dear justin thank for your previous reply
I have Adjusted My box vectors along only one pulling dimension.
I am pullling for distance of 5 nm from the center of box along Z axis
i am using the following option in editconf_d my command is as follows
./editconf_d -f
Lara Bunte wrote:
Hi
I have a geometry in a textfile which looks like that:
N 2.823790 -0.0418930.737832
C 3.563329 -1.1413070.332899
O 4.781032 -1.1659540.346660
You see the atom and then three spatial
The current scheme for the proper dihedral scaling for free energy
simulation assumes the same multiplicity for both states. This is
problematic if we want to change, e.g., a CH3 group to an NO2 group. We can
manipulate the topology file to make it right. However, it is not general
and can be
Hi All,
I am trying to use g_msd for a system of bilayer+protein+ions (water removed
for convenience).
I have a {.dcd} file with say, 3 frames. Each frame was written at 5000
steps (i.e., frame saved 10ps each ). Thus, whole trajectory corresponds to
300,000 ps (300ns). I got {.tpr} file
g_msd -f noWAT_all_sys3_xray_1ns_300ns.dcd.xtc -s noWAT_sys3_xray.tpr -o
msd.xvg -rmcomm -b 0 -e 3 -beginfit 10 -endfit 30 -trestart 10
-lateral z
So the last frame you want it to read from the trajectory is at 30ns, but you
want it to begin the fitting from 100ns?
The -b -e and
Thanks for the reply Justin,
In theory, that should work. Please post the entirety of your .mdp file.
Have you done any prior equilibration, or have you moved straight into
annealing? I would suggest a restrained NVT before applying NPT or
annealing
when using the restraints.
Yes I
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