Hello sir,
On giving gmxdump its giving me an error saying segmentation fault.My box
size is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5 timesteps
and with columb type=PME. I read from mailing list that PME calculations
requires large amount of memory space.Is this an issue with
Could you tell me, please.
What's directions need the programm pdb2gmx to use external .itp files, for
example martini_v2.1.itp (Coarse Grained Force Field)?
How is it to do ?
I use GROMACS v3.3.2 and OPLSAA Force Field.
Igor
___
gmx-users
varsha gautham wrote:
Hello sir,
On giving gmxdump its giving me an error saying segmentation fault.
99.9% of the time there is more information available. Check your
stdout, stderr and the .log file.
My
box size is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5
timesteps and
bhf70 wrote:
Could you tell me, please.
What's directions need the programm pdb2gmx to use external .itp files,
for example martini_v2.1.itp (Coarse Grained Force Field)?
How is it to do ?
There should be instructions accompanying that force field wherever you
got it from.
There's
Hi,
Independent of any other problems you might have, gmxdump should never give a
segmentation fault.
Could you mail me the tpr file?
Which version of Gromacs are you using?
Berk
Date: Mon, 16 Feb 2009 12:57:50 +0400
From: varsha.gautha...@gmail.com
To: gmx-users@gromacs.org
Subject:
There is a script in vmd to do it.
Catch ya,
Dallas Warren
A polar bear is a Cartesian bear that has undergone a polar
transformation
On 16/02/2009, at 3:30 PM, Chih-Ying Lin chihying2...@gmail.com
wrote:
HI
after creating the box, and write it into .gro file.
when i try the .gro file
It is possible to set an example ?
bhf70 wrote:
Could you tell me, please.
What's directions need the programm pdb2gmx to use external .itp files,
for example martini_v2.1.itp (Coarse Grained Force Field)?
How is it to do ?
There should be instructions accompanying that force field
What do you mean by directions?
in your topology file you have to include the file martini_v2.1.itp
as you would do for any other force field!
On Feb 16, 2009, at 11:07 AM, bhf70 wrote:
It is possible to set an example ?
bhf70 wrote:
Could you tell me, please.
What's directions need the
fpri...@nimr.mrc.ac.uk wrote:
I did not stop the simulation manually and it did not give a segmentation fault
message, but something else that I have never seen before (and actually, I am
still not understanding the error message).
Now I'm running the dynamics on my machine, instead of running
Hi,
You should be much more precise in describing your problems.
gmxdump does not seem to give a segv at all.
Also you did not mail me your Gromacs version.
mdrun immediately gives a warning:
Warning: 1-4 interaction between 1 and 28 at distance 0.982 which is larger
than the 1-4 table size
Hi all Gromacs users:
These days I read the codes about domain decomposition of Gromcas-4.0.
It seems that every node which is used to deal with one real space
domain has all of the molecules' information as in the particle decomposition.
Is my comprehension right? And if it's wrong how is
Hi
I'm trying to create an oscillating electrical field in my simulation,
and I was hoping that someone who had successfully done this in the
past could please offer some advice on the choice of parameters in my
mdp. Eventually, I would like to create a system with oscillating
fields
If your box is very big, VMD may run out all your computer's memory and
crash. You can copy your GRO file and erase some water molecules in the
middle of the GRO file copy, for you see the extremes of your water box.
Kind regards.
--
From: Mark
package require pbctools
pbc box
should do it.
On Sun, Feb 15, 2009 at 10:29 PM, Chih-Ying Lin chihying2...@gmail.com wrote:
HI
after creating the box, and write it into .gro file.
when i try the .gro file with VMD, but the box is not shown.
how can i show the created box with VMD?
Hello, everyone,
I have some questions about ensemble. Would you please tell me about NPT or NVT
ensemble? What difference about them? And how to define in the molecular
dynamics mdp file? What ensemble does the below parameters extracted from my
mdp file?
; Berendsen temperature coupling is
I have some questions about ensemble. Would you please tell me about NPT or
NVT ensemble? What difference about them?
http://wiki.gromacs.org/index.php/Molecular_Dynamics_Simulations
Catch ya,
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University
A polar bear is a
Hello,
I'm interested in setting up a simulation in Gromacs based on a procedure
from an interesting paper. The paper (available here:
http://tinyurl.com/cp4qbu) describes simulating peptides confined to inert
spherical pores.
I'm not yet an advanced Gromacs user, and so I was hoping someone in
OK, well I got this wrong.
If you want to extend or continue a simulation that has completed, you still
have to use tpbconv. It is used to change the number of steps, then you feed
that into mdrun with the checkpoint file. The only time you don't need tpbconv
now is with a crashed
When using checkpoint files to continue a run, mdrun overrides the output file
names specified by putting .part before the file extension.
I don't want it to do that, since I have already told it how I want the output
files to be named.
Is it possible to stop that happening?
Catch ya,
Dr
Dallas B. Warren wrote:
When using checkpoint files to continue a run, mdrun overrides the output file names
specified by putting .part before the file extension.
I don't want it to do that, since I have already told it how I want the output
files to be named.
Is it possible to stop
Justin,
When using checkpoint files to continue a run, mdrun overrides the output
file names specified by putting .part before the file extension.
I don't want it to do that, since I have already told it how I want the
output files to be named.
Is it possible to stop that
One option is to avoid checkpoint files all together. I personally use
a grompp/mdrun cycle of ~2h segments that was historically done in
order to utilize the -sort -shuffle options to gromacs 3. I found it
simpler to keep on doing the exact same thing in gromacs 4, even
though I no longer
Chris,
One option is to avoid checkpoint files all together. I personally use
a grompp/mdrun cycle of ~2h segments that was historically done in
order to utilize the -sort -shuffle options to gromacs 3. I found it
simpler to keep on doing the exact same thing in gromacs 4, even
Date: Tue, 17 Feb 2009 16:59:42 +1100
From: dallas.war...@pharm.monash.edu.au
Subject: RE: [gmx-users] Possible to stop mdrun changing file names when
usingcheckpoint files?
To: gmx-users@gromacs.org
Chris,
One option is to avoid checkpoint files all together. I personally use
a
Hi
Thank you for your reply, Berk. I mean that every node has
the topology of the whole system. Originally I thought every
node has the positions and other properties(information in my
last e-mail) of the atoms. I made a mistake obviously.
But now, I don't know how do you store the
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