Dear Berk,
Thanks for the reply. I have read through your
paper. I have still some doubts.
When used tcafś I got files called
tcaf_all.xvg tcaf_fit.xvg tcaf.xvg visc_k.xvg ( all default names).
I think, the file which I should use for fitting, using the fo
Dear Berk and David,
Thank you very much for your
appropriate and informative replies. I tried another method (traverse current
method) to calculate the shear viscosity ( a non equilibrium method, which has
been described in Berkś paper : Journal of C
813 13.4652 101.366
9.96016 13.7012 100.249
-
regards,
Jes
On Thu, 12 Mar 2009 David van der Spoel wrote :
>JMandumpal wrote:
>>Dear GROMACS users,
>>
>> As explained in
Dear GROMACS users,
As explained in the manual ( page 139, section
6.5/3.3.3) I would like to calculate viscosity of my system ( water) using
g_energy. I opted(40 Mu-X ) from the g-energy selection. But the unit
written on the Y axis of the corresponding xvg file
Dear Xavier and Jochen,
Thank you for the suggestions: it works well now.
Jes.
On Mon, 27 Oct 2008 Xavier Periole wrote :
>On 27 Oct 2008 06:36:09 -
> "JMandumpal" <[EMAIL PROTECTED]> wrote:
>> Dear GROMACS users,
>>
>>I have got a problem while
Dear GROMACS users,
I have got a problem while running a simulated anealing simulations, using
GROMACS 3.3.3 version, of pure water:
the task:
I want to cool the system (water- 500 molecules) from 360 K to 0K in 100ps time
( fast cooling). For that I used the following script:
title
Dear GROMACS users,
A method to locate glass transtion temperature of liquids is reported by
Stanley et al, PRL 2004, 93, pp 047801: system is cooled initially and then is
heated , in the range 0K-400K, in a "modified" NVT ensemble. (Total energies of
the system with respect to temp. is plotte
Dear Manoj,
Here is the script, for running parallel, which I am using. You may need to
change it according to your machine-specifications.
--script for GROMACS 3.3.3-
#!/bin/bash
#PBS -l vmem=8gb
#PBS -l jobfs=10GB
I think, after creating an index file, you can edit it manually clubbing both
Phosphorius and Oxygen atoms together ( considering as a single group). Then
specify this group while doing analysis.
On Wed, 16 Jul 2008 minnale wrote :
> Thanks for the reply, may be this is trivial question to
I think, setting tc groups = system will solve this issue.
On Thu, 17 Jul 2008 Justin A.Lemkul wrote :
>For warnings/errors, etc. please check the archive and wiki before posting. I
>just responded to a similar issue a few days ago:
>
>http://www.gromacs.org/pipermail/gmx-users/2008-June/
Disable Temperature and Pressure coupling parameters in your script and
variables related to them as well.
Tcoupl = no
Pcoupl = no
On Wed, 09 Jul 2008 beibei wrote :
>Hi, all
>How to define NVE ensemble in mdp file? thanks.
>
Dear Gayen,
It stands for different atom types of the same element.
For instance, in all atom OPLS parameter model for acetone, following atom
types are being used.
CT, 0_2, C_2 and HC for methyl carbons, keto oxygen, carbonyl carbon and methyl
hydrogens respectively. Indeed, CT( for methyl
Dear list,
When I changed the time step to 1fs, the simulations were successful. What
could be wrong with timestep 2.0 fs. I am using GROMAXS version 3.3.3
regards
Jes
On Wed, 28 May 2008 JMandumpal wrote :
>Dear list,
>
>I was running AA acetone with tip4p water for calculatin
Dear list,
I would like to simulate aqueous acetone system using UA OPLS
potentials. I chose the following atoms types, given below (TABLE ONE),
for acetone, with united atom for Methyl groups.
TABLE ONE
Dear list,
The OPLS parameter for S in DMSO is zigma 0.395 and epsilon 3.56 A
( JACS 1996, 118, 4175-4180)
But in the ffoplsaanb.itp (/gromacs/3.3.2-dp/share/gromacs/top) it is given as
below:
-
name bond_typemass
Dear list,
Since the unit is not printed in the .xvg file
generated by the module g_msd in GROMACS 3.3.2 version , I would like to know
the unit of diffusion coefficient calculated. Is it in cm^2/ sec or m^2/sec?
regards,
jes
__
Hi Markus,
Thanks for the reply. It worked fine.
Jes
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (u
tat
> (artificially!) fixes the energy loss.
>
> The correct way is to set rlist > rvdw.
>
>
>Cheers,
>markus.
>
>--
>Halli delendum est.
>
>On Apr 3, 2008, at 13:00 , [EMAIL PROTECTED] wrote:
>
>>Date: 3 Apr 2008 08:12:40 -
>> From: "JMan
Spoel wrote :
>JMandumpal wrote:
>>Dear list,
>>
>> These are the energy I obtained running 60ps NVE of 500 TIP5P water
>> molecules- I still wonder why the energy has not been converged even having
>> run for 160 ps in total (100 NVT + 60 NVE).
>>
Dear list,
These are the energy I obtained running 60ps NVE of 500 TIP5P water
molecules- I still wonder why the energy has not been converged even having run
for 160 ps in total (100 NVT + 60 NVE).
100.00 -15887.623027
101.50 -15887.961065
103.00 -15894.289055
Dear Mark,
Thank you very much for the reply.
Well I used the following job script:
#!/bin/bash
#PBS -l vmem=800MB
#PBS -l ncpus=4
#PBS -l jobfs=10MB
#PBS -l software=gromacs
#PBS -l other=mpi
#PBS -q express
#PBS -wd
module load gromacs/3.3.2
order to run NVE.
regards,
Jestin
On Fri, 28 Mar 2008 JMandumpal wrote :
>Dear gromacs users,
>
>
>I ran 100ps equilibraion, NVT, prior to running 60ps NVE to check the energy
>conservation with different timesteps: 1.0fs, 1.5fs and 2.0fs, but these NVE
>simulations seem not to c
Dear gromacs users,
I ran 100ps equilibraion, NVT, prior to running 60ps NVE to check the energy
conservation with different timesteps: 1.0fs, 1.5fs and 2.0fs, but these NVE
simulations seem not to converge even after. Following is the command I used
for running 60ps NVE :
---
>Dear all,
>While running a job, since there was space problem I could not write the xtc
>files. Now when I do the analysis and use the trr file it reports the >time
>values after every 5ps i.e. 2000, 2005, 2010 etc. However I wish to >write the
>xtc file using trjconv such that the timestep
Rob,
I wonder whether you have got the flexible water model, TIP5P. I want to run
simulations using the flexible TIP5P water model. Well, how does the results
from the MD be affected if I use rigid water models in place of a flexible one?
regards
Jestin
On Thu, 06 Mar 2008 rob yang wrote
Dear list,
I ran EM (energy minimisation) of TIP5P water
model using gromacs/3.3.2 version. My output says : Steepest Descents converged
to Fmax < 100 in 427 steps. Moreover, my output.gro file looks ok after the
run. But in the directory, there were some file
Dear Gromacs users,
I built .tpr file prior to energy minimisation of box of tip5p water molecule.
I received the output like this:
calling /lib/cpp...
processing topology...
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 33252
Hello Mauro,
Please have a look at here,
http://www.ime.unicamp.br/~martinez/packmol/
regards
Jestin
On Thu, 29 Nov 2007 Mauro Puppett wrote :
>
>Hi all!
>I've to run a simulation in a box filled with chloroform.
>I'm using GROMACS with amber99 force field but I'm a beginner and I have no
Dear users,
What I see the difference between the .gro file given at the examples in the
tutor directory and my own .gro file is that
the last lines gives 0.000 0.000 0. in my file and in the examples it is
not.
I assume it is the dimension of the box, isn' it?
I built up the gro file u
Dear Gromacs users,
Thanks for the messages.
Tsjerk,
I was not aware that capital letters denote unpolite. I just used them to
highlight the problem so others can easily pick out. Thanks for the suggestions
as well.
I modified the file:
***
Dear Justin,
I made some changes in my .mdp file, but the result is same.
My box size, as mentioned in the previous mail, is 20.1 A. The cut off I used
is 8 angstrom.
I attach the input file here.
**
cpp= /lib/cpp
define = -DPOSRES-DF
Dear Justin,
It seems, the given link which was directed to a post where I got contents of
ENERGY MINIMISATION FILE ".mdp" in my previous mail is not the right one, so I
paste its content here.
***
Geraudis Mustelier gera at ict.c
Dear Justin,
Thanks for the response.
This is my input file (em.mdp) which contains parameters for doing energy
minimisation.
cpp= /lib/cpp
define = -DPOSRES -DFLEX_
constraints= none
morse = no
integrator = steep
nsteps = 2000
; Energy minimizi
Dear Gromacs users
When I run Energy minimisation using the command,
grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr, I received the following
error message.
**
processing coordinates...
double-checking input for internal consistency
Dear Gromacs users,
Using the command, grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr, I wanted
to build up tpr file for the simulation, but failed to do so.
I received the error message :
Moleculetype SOL contains no atoms.
I paste my top files and .itp file below
*
The top file is
#include "ffgmx.itp"
#include "tip5P.itp"
[ system ]
Pure water
Dear Gromacsians,
Using the command, grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr, I wanted
to build up tpr file for the simulation, but failed to do so.
I received the error message :
Moleculetype SOL contains no atoms.
I paste my top files and .itp file below
***
Dear Gromacs users,
When I tried to build up .tpr file for running energy minimisation, I
encountered some problems:
This is the command I used:
grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr
and I received the following error message:
Fatal error:
Invalid order for directive system,
Dear David,
I didn't get the desired box length when I tried to use editconf command ( I
took the tip5p box from gromacs/tutor directory) . Then, I tried editconf
command to generate .gro file using myown water box. It worked!!
Still, there is a problem. How can I create .ndx file?- I tried
QUESTION WITHDRAWN
QUESTION WITHDRAWN
***88
I think, I must use the command
editconf *.gro bt dodecahedron d 0.5 o *.gro
to generate the box of desired length.
I didn't notice this command, hence was the confusion. Sorry for the
disturbance and I
Thanks David for the reply.
I was able to build topology file from the info given in
the top directory. In contrast to the .gro file for TIP5P box, containing 516
water molecules, given at the top directory, I need a specific box size with
exact number of water molecules (2
Friends,
I would like to simulate a box of water (TIP5P model), with 258 water
molecules. When I tried to build up the .top, .gro and .ndx files using the
command pdb2gmx -p -i -n -o -f tip5p_W.pdb,
I got an error message : input/ output error, program aborted.
MY input structure, ie, tip5
Dear GROMACS users,
I would like to use Glycam forcefields for sugars with TIP5P water model. Does
anyone have experience(GROMACS) simulating using GLYCAM/TIP5P?
cheers
Jestin Madumpal
___
gmx-users mailing listgmx-users@gromacs.org
http://www.g
43 matches
Mail list logo
