Anirban,
It is better to keep conversations on the gmx-user list where I
believe you found much help already.
I looked quickly at your EM.gro file. There several issues that
you should have picked your self quite easily using VMD.
1- there are 3 empty line in your gro file: lines 204, 2253
Hi
I used grompp command but follow fatal error appeared:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section settles in a
part belonging to a different molecule than you intended to.
In that case move the settles section to the right
Hi,
I have LiCl solutions, SPCE and TIP4P2005 water models and OPLS. It worked
for both models with one concentration, this one also works with SPCE, but
using TIP4P2005 stops writing somehow. The program mdrun does not crash
for a day even, seems to run, but the .edr and .trr files are empty,
-- Forwarded message --
From: leila karami karami.lei...@gmail.com
Date: Tue, Nov 3, 2009 at 1:50 PM
Subject: grompp
To: gmx-users@gromacs.org
Hi
I used grompp command ( grompp -f -c o -p c -o t.tpr) but a mdout.mdp file
is created and follow fatal error appeared:
Atom index
Hi all,
I've already simulated 27 organic molecules in a cubic solvent box. Now
I would like to calculate the SAS of this system. I've a tpr and a trr
with only the molecules inside (without water).
I'm using gromacs 4.0.5.
I've added the box dimension infos to the trr using the command:
trjconv
andrea carotti wrote:
Hi all,
I've already simulated 27 organic molecules in a cubic solvent box. Now
I would like to calculate the SAS of this system. I've a tpr and a trr
with only the molecules inside (without water).
I'm using gromacs 4.0.5.
I've added the box dimension infos to the trr
leila karami wrote:
Hi
I used grompp command but follow fatal error appeared:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section settles in
a part belonging to a different molecule than you intended to.
In that case move the settles
Hello Users,
I am trying to install gromacs on windows and find lot of problems. First I
have installed Cygwin with gcc, gdb and make packages. Then FFTW-3.2.2 and
configure it but when I used make and make install commands but some
directories leave as it is. When configure gromacs-4.0.5 then it
dear justin
I use amber force field in gromacs.can this subject make such error :
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section settles in a
part belonging to a different molecule than you intended to.
In that case move the settles
pawan raghav wrote:
Hello Users,
I am trying to install gromacs on windows and find lot of problems.
First I have installed Cygwin with gcc, gdb and make packages. Then
FFTW-3.2.2 and configure it but when I used make and make install
commands but some directories leave as it is. When
leila karami wrote:
dear justin
I use amber force field in gromacs.can this subject make such error :
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section settles in
a part belonging to a different molecule than you intended to.
In that
Hi everyone !!
I am having a problem using pdb2gmx command. Using the command on my input
pdb file, it results saying Fatal error: Atom O in residue CCMT 1 not found
in rtp entry with 38 atoms while sorting atoms. I do not have only O
either in input pdb file or in rtp file. and its O and not 0
dear justin
Fatal error:
[ file spc.itp, line 46 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section settles
in a part belonging to a different molecule than you intended to.
In that case move the settles section to the right molecule.
I
leila karami wrote:
dear justin
Fatal error:
[ file spc.itp, line 46 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section settles
in a part belonging to a different molecule than you intended to.
In that case move the settles section
Hi,
The preprocessor cuts away all parts of the [ atoms ] section in your
spc.itp when you use the amber forcefield. I believe there is another
version of spc.itp that comes with the amber port. Try using that one,
or write your own entries in the existing file between a set of #ifdef
pawan raghav wrote:
I am attaching the config file which is generated on my system by using
fftw-2.1.5. Please notify me where is the mistake.
For future reference, ZIP archives can be inconvenient for some users (we use
primarily Mac and Linux systems). There is no need to zip up a log
Hi, David,
I used Berendsen thermostat and a bigger tau_t=1ps to redo the simulations.
The general conclusion is the same. The std err is the same in both
packages. And during each simulation, the integration time does not
change. Details below:
Integration time step 1fs:
Please keep all correspondence on the gmx-users list. I do not advertise myself
as a private help service, and furthermore, you always stand a better chance at
getting a response by posting to the list.
Is this the post you're referring to?
Peng Yi wrote:
Hi, David,
I used Berendsen thermostat and a bigger tau_t=1ps to redo the simulations.
The general conclusion is the same. The std err is the same in both
packages. And during each simulation, the integration time does not
change. Details below:
Integration time step 1fs:
Thielges, Sabine wrote:
Reading file md_20_100_s_IP_beta.tpr, VERSION 4.0.3 (single precision)
Reading checkpoint file md_20_100_s_IP_beta_prev.cpt generated: Sat Oct 31
12:34:46 2009
---
Program mdrun.MPI, VERSION 4.0.3
Source code
I solved the problem.
The command that works is:
trjcat -f md00.xtc md01.xtc ... md0N.xtc -o out00.xtc out01.xtc ...
out0N.xtc -s replica_index.xvg
Jianhui
Date: Tue, 03 Nov 2009 10:24:12 -0500
From: Justin A. Lemkul jalem...@vt.edu
Subject: [gmx-users] Re: trjcat -demux problem
To: Jianhui
Paymon Pirzadeh wrote:
Hello,
To restart a run for continuation, which .cpt file should be used? the
one with the outputname.cpt or the outputname_prev.cpt?
The most recent. The _prev name indicates that it is a backup in case the
newest one fails or has a problem. Run gmxcheck on each
I turned off the torsion interaction. The difference between Lammps and
Gromacs at integration time step 2fs was reduced. Details below:
A melt of 240 n-octane (united-atom model), NVT, T=300K, V=55.46nm^3.
Both Lammps and Gromacs use berendsen thermostat with tau_t=1ps.
Integration time
Hi,
I know that g_dist gives the distance between the center of masses of two
groups. But, I wanted to know whether it is possible to calculate angle
between center of masses of three groups or not . I am not sure whether g_angle
can calculate the angle between center of masses of three
Hello,
To restart a run for continuation, which .cpt file should be used? the
one with the outputname.cpt or the outputname_prev.cpt?
Payman
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Please
Chandan Choudhury wrote:
Hi everyone !!
I am having a problem using pdb2gmx command. Using the command on my
input pdb file, it results saying Fatal error: Atom O in residue CCMT 1
not found in rtp entry with 38 atoms while sorting atoms. I do not have
only O either in input pdb file or in
jagannath mondal wrote:
Hi,
I know that g_dist gives the distance between the center of masses of
two groups. But, I wanted to know whether it is possible to calculate
angle between center of masses of three groups or not . I am not sure
whether g_angle can calculate the angle between
Chandan Choudhury wrote:
My complete input file is
ATOM 1 NCCMT 1 -2.521 -2.813 2.083 0.00 0.00
ATOM 2 CA CCMT 1 -2.925 -1.739 1.166 0.00 0.00
ATOM 3 CCCMT 1 -1.711 -0.842 0.859 0.00 0.00
ATOM 4 CB CCMT 1 -4.034 -0.895
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