Hi there,
while running gromacs in parallel with double precision, during grompp_d I
am getting following warning in output file along with other status..
...
...
...
WARNING 1 [file 1XU9_A.top, line unknown]:
The largest charge group contains 12 atoms.
Since atoms only see each other when
You seem not to get it... I specifically chew out for you that you
need to give a listing using the command ls -l. That will also show
what the size of the file is. This is completely pointless this way!
Also, you only now state the command you gave.
Now, rereading the first mail, it also said
vivek sharma wrote:
Hi there,
while running gromacs in parallel with double precision, during
grompp_d I am getting following warning in output file along with
other status..
...
...
...
WARNING 1 [file 1XU9_A.top, line unknown]:
The largest charge group contains 12 atoms.
Since atoms
vivek sharma wrote:
Hi Jochen,
Thanks for your response. That was some syntax error, now I am getting
only single .edr file.
Is there any restriction in mdp file parameters while running it in
parallel mode ?
And, is it necessary to run energy minimization and position
restraining before
I'm sure I have, in the past, found a way to use trjcat/trjconv to overwrite a
bad frame with a good one. From memory, I had to convert the area around the
bad frame to pdb/gro (for some reason that worked where normal tools didn't),
open up the files, rewrite several bad frames (just copied
Good day to you!
I'm new to MD and this is my first time bugging you with issues I don't seem to
be able to solve on my own (using the archive and the manual), so I hope you
bare with me and can possibly offer me a sanity check or some alternative
approaches to my problem.
As I have already
Using google returns no good results, would anybody help me about this?
Configure grace did not succeed..
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Ross KK Leung wrote:
Using google returns no good results, would anybody help me about this?
Configure grace did not succeed….
Having no idea what you're doing, I doubt anyone here can provide any useful
advice. Furthermore, this list is for Gromacs-related questions, not Grace.
Try
Ted Fischer wrote:
Good day to you!
I'm new to MD and this is my first time bugging you with issues I don't seem to
be able to solve on my own (using the archive and the manual), so I hope you
bare with me and can possibly offer me a sanity check or some alternative
approaches to my
Then how would you analyze the MD results? Because Gromacs output is an xvg
file and Google returns very few results about it...
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Justin A. Lemkul
Sent: Thursday, August 28, 2008 5:54 PM
To: Discussion list
Ross KK Leung wrote:
Then how would you analyze the MD results? Because Gromacs output is an xvg
file and Google returns very few results about it...
I'm not saying you shouldn't use Grace. All you've told us is that you could
not configure Grace. Without any details (system type,
Hi,
On Thursday, 28. August 2008, Ross KK Leung wrote:
Then how would you analyze the MD results? Because Gromacs output is an xvg
file and Google returns very few results about it...
it is a plain text file.
Per default xmgrace files are written by gromacs
Hey,
And on top of that, you don't need to get any of these grace related
tags which make it 'xvg'. You can use the flag -noxvg with about any
tool and get nothing but the raw data. (One could also use grep -v
[EMAIL PROTECTED] something.xvg to remove the grace directives).
And that makes a
Using google returns no good results, would anybody help me about this?
Configure grace did not succeed….
You are absolutely right. Install MOTIF.
What's the problem?
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL
Dear
I have a box with 2 different kind of solution and one protein. Actually,
I minized my box in each step which i add matter to box. After
minimization of my system I run it for 10 ns. unfortunately after 1.3 ns
one of my solution dissapear. eg, I have hexan organic solvent, water and
protein,
Hi all,
I am new to gromacs, I am interested in calculate Hydrogen bonds of my
protein. So I have issued the *g_hbond command like this
g_hbond -f .xtc -s .tpr -n .ndx(Index file contain all residues mainchain+H
atoms) -num .xvg -g .log
its showed
Program g_hbond, VERSION 3.3.1
Source
minnale wrote:
Hi all,
I am new to gromacs, I am interested in calculate Hydrogen bonds of my
protein. So I have issued the *g_hbond command like this
g_hbond -f .xtc -s .tpr -n .ndx(Index file contain all residues
mainchain+H atoms) -num .xvg -g .log
its showed
Program g_hbond, VERSION
Morteza Khabiri wrote:
Dear
I have a box with 2 different kind of solution and one protein. Actually,
I minized my box in each step which i add matter to box. After
minimization of my system I run it for 10 ns. unfortunately after 1.3 ns
one of my solution dissapear. eg, I have hexan organic
Thanks Justin for your quick reply
the g_hbond command ran succesfully and gave me .xvg file and it contain 3
columns
that is like
@title Hydrogen Bonds
@xaxis label Time
@yaxis label Number
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype
Thanks Justin for your quick reply
the g_hbond command ran succesfully and gave me .xvg file and it contain 3
columns
that is like
@title Hydrogen Bonds
@xaxis label Time
@yaxis label Number
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype
Dear all,
I am using the Louhi cluster on the Finnish IT center
(http://www.csc.fi/english) and I had the chance to test the latest beta
version of gromacs (3.99.4). First of all I have to say that it is very
fast and very scalable. Now, reliability. I have run a 2ns simulation of
a protein in
minnale wrote:
Thanks Justin for your quick reply
the g_hbond command ran succesfully and gave me .xvg file and it contain
3 columns
that is like
@title Hydrogen Bonds
@xaxis label Time
@yaxis label Number
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@
Morteza Khabiri wrote:
Dear
Thanks for your prompt reply.
In gro file everything is ok. during the run I just load my XTC file by
vmd visual software and i saw that after 1.3 ns suddenly hexan disappear
Did you restart your run after that short time? Did you change the xtc-grps
option in
Dear Users:
I am planing to do some simulations of a protein in acetonitrile using the
model of P.J. Gee (Mol. Phys. (2006) 104, 477-483). The use of this model
will introduce new atom types and new LJ parameters for those atoms. When I
define those atoms in the acetonitrile topology I need to
Dear Justin
Thanks for your helps.
--Did you restart your run after that short time? Did you change the
xtc-grps
option in your .mdp file?
no. I did not change any option and also not restart my run.
--That would be pretty strange. If they were there, then disappeared,
maybe they were not
Anthony Cruz wrote:
Dear Users:
I am planing to do some simulations of a protein in acetonitrile using the
model of P.J. Gee (Mol. Phys. (2006) 104, 477-483). The use of this model
will introduce new atom types and new LJ parameters for those atoms. When I
define those atoms in the
Morteza Khabiri wrote:
Yes. after disappear, the vmd console show an error. it is:
Error reading timestep, file does not match format.
What does gmxcheck tell you about the file? Maybe there was a hardware blip or
something that messed up a frame in the .xtc file.
As I said
Hi Justin, well, actually the problem is not only with grompp, since
my non integer charges come all the way since pdb2gmx
I used as I told:
pdb2gmx -f 1vkxdna.pdb -o 1vkxdna.gro -p 1vkxdna.top
editconf -f 1vkxdna.gro -o 1vkxdna_caixa.gro -c -d 0.9 -princ
genbox -cs -cp 1vkxdna_caixa.gro -o
Thank you for your rapidly responce David. If I use thr Gromos96 (ff43a1) it
will do it? How I check if the force field allows mixing?
Cheers,
Anthony
On Thursday 28 August 2008 01:34:30 pm David van der Spoel wrote:
Anthony Cruz wrote:
Dear Users:
I am planing to do some simulations of a
Greetings!
I am trying to perform free energy calculations on my protein system. I am
using Gromacs 3.3.3 double precision for Linux.
The grompp runs fine and the .tpr file is created, but as soon as I submit the
batch job, it dies and I receive the following error message
Back Off! I just
Ragnarok sdf wrote:
Hi Justin, well, actually the problem is not only with grompp, since
my non integer charges come all the way since pdb2gmx
I used as I told:
pdb2gmx -f 1vkxdna.pdb -o 1vkxdna.gro -p 1vkxdna.top
editconf -f 1vkxdna.gro -o 1vkxdna_caixa.gro -c -d 0.9 -princ
genbox -cs -cp
Dear Justin
Thanks for your prompt reply and guide.
As you said I checked my files with gmxcheck.
My tpr file is ok. It includes water, hexan and protein. but my edr, xtc
and trr files have problem.
Their faults are as follow:
1- for xtc: Reading frame 110 time 550.000 Fatal error:
Quoting Morteza Khabiri [EMAIL PROTECTED]:
Dear Justin
Thanks for your prompt reply and guide.
As you said I checked my files with gmxcheck.
My tpr file is ok. It includes water, hexan and protein. but my edr, xtc
and trr files have problem.
Their faults are as follow:
1- for xtc:
Dear users,
I am trying to calculate the diffusion coefficient for my protein using
g_msd. I issued the following command:
g_msd -f .xtc -s .pdb -o .xvg
It gave me the diffusion coefficient as 0.068 (+/- 0.0279) * 10^-5 cm^2 s^
-1 (for my whole system). The shape of the plot is not linear
Thanks Justin for your reply
I am interested to get file which contain how many hydrogen bonds are there in
my protein and the bonds present between which atoms?
Is there anyway to get this file
can you please tell me,
Thanks in advance for your kind suggestion
On Thu, 28 Aug 2008 Justin
Hello all,
Sorry to bother you, I have a question about the content in the file
atm-pair.out file which is generated by the command g_mindist. Here is several
lines of the file:
0.00e+00 114 72
1.00e+01 114 72
2.00e+01 85 66
3.00e+01 85 65
4.00e+01 82 66
5.00e+01
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