Hi Everyone,
I have been trying to calculate diffusion coefficient for water. I am trying
to reproduce the numbers published in journal papers.
I am using SPCE water model. I use the g_msd analysis tool.
g_msd -f traj.trr -n index.ndx -s npt.tpr -b 2 -e 8
I use a box of volume 6x6x6 nm^3 which h
Hi all,
I am trying to save the conformation of my protein after 10ps
simulation .. I am getting the following error :-
Software inconsistency error:
Not supported in write_sto_conf
Can anybody tell me how to fix this error ..
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinforma
Hi all,
I am trying to save the conformation of my protein after 10ps
simulation .. I am getting the following error :-
Software inconsistency error:
Not supported in write_sto_conf
Can anybody tell me how to fix this error ..
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformat
Hi,
you already have your solution at hand.
On 10.02.2010, at 10:05, Amit Choubey wrote:
> Hi Everyone,
>
> I have been trying to calculate diffusion coefficient for water. I am trying
> to reproduce the numbers published in journal papers.
> I am using SPCE water model. I use the g_msd analy
bharat gupta wrote:
Hi all,
I am trying to save the conformation of my protein after 10ps
simulation .. I am getting the following error :-
Software inconsistency error:
Not supported in write_sto_conf
Can anybody tell me how to fix this error ..
Not without more information, like the Gr
Hi all,
I met a problem when I try to use trjcat to connect the trajectory files of
REMD. I used 16 replicas for my simulation, and used demux.pl perl script to
generate the replica_index.xvg and replica_temp.xvg. Then I used trjcat -f
xtc_*.xtc -demux replica_index.avg, however got an error i
tekle...@ualberta.ca wrote:
Dear Justin,
First of all thank you for your help..
I have developed the toplogy file for my molecule using the PRODRG
server. But the topology did not include properly the carboxylic acid
functional group ( with proton) instead the software assumes both
oxygens
10 ps is too short of a trajectory, even for such a large system (for pure
water it is considered large). i would guess that it is a typing-error and
you ran for 10 ns?
omer.
On Wed, Feb 10, 2010 at 11:05, Amit Choubey wrote:
> I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I
>
zuole wrote:
Hi all,
I met a problem when I try to use trjcat to connect the trajectory files
of REMD. I used 16 replicas for my simulation, and used demux.pl perl
script to generate the replica_index.xvg and replica_temp.xvg. Then I
used trjcat -f xtc_*.xtc -demux replica_index.avg, howeve
Sorry for the delay in replying back. I start the job using the
following script file:
#$ -S /bin/bash
#$ -l h_rt=47:59:00
#$ -j y
#$ -pe mpich2 8
#$ -cwd
cd /home/jwillia4/GRO/gromacs-4.0.7/JJW_003/PH_TORUN
/home/jwillia4/GRO/bin/mpirun -np 8 /home/jwillia4/GRO/bin/mdrun_mpi
-v -s md.tpr
On 02/10/10, Jennifer Williams wrote:Sorry for the delay in replying back. I start the job using the following script file:#$ -S /bin/bash#$ -l h_rt=47:59:00#$ -j y#$ -pe mpich2 8#$ -cwdcd /home/jwillia4/GRO/gromacs-4.0.7/JJW_003/PH_TORUN/home/jwillia4/GRO/bin/mpirun -np 8 /home/jwillia4/GRO/bin/
Hi all
I wanna know that for how long shall I run the energy minimization
step to minimize my modelled protein structure .. and what all
parameters shall I look for the minimized structure - rms , rmsf ,
potential , g_energy . In g_energy total energy and potential both
have to be checked ...
--
bharat gupta wrote:
Hi all
I wanna know that for how long shall I run the energy minimization
step to minimize my modelled protein structure .. and what all
parameters shall I look for the minimized structure - rms , rmsf ,
potential , g_energy . In g_energy total energy and potential both
hav
Hi ,
I want to install gromacs 4.0.7 in double precision in a 64 bit Mac
computer with 8
nodes.
I got the lam7.1.4 source code files and installed them using the following
commands
./configure --without-fc ( it was giving an error for the fortran compiler)
make
make instal
so how shall i proceed now ... can u guide ??
--
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/search before posting!
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bharat gupta wrote:
so how shall i proceed now ... can u guide ??
No. If you have a specific question, then ask it, but this forum shouldn't be
viewed as a tool to teach you everything about how to run simulations. I would
suggest that you consult any of the numerous textbooks about simu
Ok, here's my topology file:
; Include forcefield parameters
#include "ffgmx.itp"
#include "lipid.itp"
; Include Lipid Topologies
#include "popc.itp"
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct
Dear gromacs users,
I am trying to collect trajectories corresponding to each temperature by
using trjcat with demux.
There were similar issues posted earlier, but I do not see the solution on
the problem I am facing following:
I have 64 replicas simulated using namd in dcd trajectory format a
I just used this topology in conjunction with popc128a.pdb (with some naming
adjustments to match the topologies), and everything worked fine. I am using
version 4.0.5, as well.
Are you running grompp on a local workstation, or on a remote filesystem? I
have noticed sporadic, unpredictable
hello
How can we calculate binding free energy and electrostatics potential for
ligand-protein complex?
which parameter is required in mdrun input file for that?
I tried online manual but did not get output.
It is appriciable if any body have idea
Thanks in advance
Regards
Pawan Gupta
--
Dears,
One questions about pair interaction. I mean the one defined in the
topology files under the [ pairs ].
They interaction with plain electrostatic, meaning without shift, switch
function applied to it. If it was possible to change this, it would be
pretty nice, unless there are specific u
pawan gupta wrote:
hello
How can we calculate binding free energy and electrostatics
potential for ligand-protein complex?
Binding free energy may require the calculation of PMF or the use of
thermodynamic cycles (both somewhat complicated procedures). If you want the
nonbonded energies
Hello all,
After minimizing the energy of my system of 200 particle coordinates of
box dimension 3.5 nm to an acceptable value, I proceeded to doing mdrun but
got the error message:
"Source code file: nsgrid.c, line: 348. Fatal error: Number of grid cells is
zero. Probably the system and box
Well ... the answer is yes: pairs interactions are scaled by
if epsilon different than 1.0 is defined in the mdp file ...
but easier to fix that the shift/switch thingy ...
Another point (more scary) is that using fudge LJ = 0.0 does not turn
off the pairs LJ interactions; fudge QQ does for elec
Lum Nforbi wrote:
Hello all,
After minimizing the energy of my system of 200 particle coordinates
of box dimension 3.5 nm to an acceptable value, I proceeded to doing
mdrun but got the error message:
"Source code file: nsgrid.c, line: 348. Fatal error: Number of grid
cells is zero. Pr
Hi all,
i think my question is kind of trivial but i'll ask it any way:
suppose you have atoms that are arranged on the XY plane in a square
lattice arrangment with a spacing of 1. you bond them , add angles etc. and
now you want to add proper dihedral angles using function 1.
What i know, is th
I have a question about the procedure for running a parallel
simulation on more than 12 processors using GROMACS 4.0.7.
I understand that partitioning the PME calculations and PP
calculations improves performance, and that there is an initial
automated "guess" at deciding how many processor
Hi,
Have a look at g_tunepme on the gromacs web site or on google. It does
this fine tuning for you.
It is pretty good
On Feb 10, 2010, at 21:09, Warren Gallin wrote:
I have a question about the procedure for running a parallel
simulation on more than 12 processors using GROMACS 4.0.7.
Hi all,
I would really appreciate if someone can help me with the "group for
output" option on g_cluster.
When I use g_cluster, it asks me to select two groups. A gourd for fit
and RMSD calculation and a group for output:
Select group for least squares fit and RMSD calculation:
Group 0 (
Dear gromacs users,
I am trying to collect trajectories corresponding to each temperature by
using trjcat with demux.
There were similar issues posted earlier, but I do not see the solution on
the problem I am facing following:
I have 64 replicas simulated using namd in dcd trajectory format a
Segun Jung wrote:
Dear gromacs users,
I am trying to collect trajectories corresponding to each temperature by
using trjcat with demux.
There were similar issues posted earlier, but I do not see the solution
on the problem I am facing following:
Like what? It will save time if you can
Dear Gromacs community,
I modified the pull code in GROMACS to apply forces on atoms that are in
a certain region of
space. It compiles error free and runs fine to give me the expected
results. I then recompiled with
mpi support. The cluster I am using has 8 cores/processors per node. When
As a follow up to my post (pasted below), I am providing some more details.
1. I am applying forces on heavy atoms (water oxygens and protein
non-hydrogens).
2. I tried switching of SHAKE. Results improve marginally, but the 8
processor data are still wrong.
3. There is no pressure coupling
On 11/02/10 06:52, Amir Marcovitz wrote:
Hi all,
i think my question is kind of trivial but i'll ask it any way:
suppose you have atoms that are arranged on the XY plane in a square
lattice arrangment with a spacing of 1. you bond them , add angles etc.
and now you want to add proper dihedral a
On 11/02/10 01:55, sarbani chattopadhyay wrote:
Hi ,
I want to install gromacs 4.0.7 in double precision in a 64 bit Mac
computer with 8
nodes.
I got the lam7.1.4 source code files and installed them using the
following commands
./configure --without-fc ( it was giving an error for the fortran co
Hello gmxusers !!
I am simulating a protein and it is bound to ATP.
Simulation of protein alone (without) works fine. Solely ATP simulation too
works. But the problem arises on adding ions to the protein + ATP (1QHH.pdb)
file.
Error:
$ genion -s em.tpr -o ion.pdb -p topol.top -np 48
WARNING: tur
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