I think what you really need is not Gromacs.
For example, you can use UCSF Chimera to get alignment and RMSD between two
PDBs.
dawei
On Wed, Jan 23, 2013 at 10:38 AM, Shima Arasteh shima_arasteh2...@yahoo.com
wrote:
Hi,
Is it possible to get RMSD of 10 different pdb files by GROMACS?
Dear All
I tried to run MD with ensemble based distance restrain. I set
disre=Ensemble and use -multi command argument in mdrun, according to the
manu. However, gromacs4.6 give me an error Sorry, distance restraints with
ensemble averaging over multiple molecules in one system are not functional
Dear Mark
Here it is some information that may be useful. I checked all my -pd, with
distance restraints MD runs. It seemed that crash usually happened when
protons and the carbon they attached were in different processors.
best,
dawei
On Thu, Dec 13, 2012 at 4:12 PM, Da-Wei Li lida
I think the same way as you. They do bring in errors but this is acceptable
in normal MD because we already have lots of approximations. BTW, -sum has
been dropped from 4.5, in other words, Gromacs won't calculate global
Energy every step by default now.
dawei
On Fri, Dec 14, 2012 at 9:46 AM,
off the restraints is not a proper solution (and
particularly not without adjusting the time step accordingly) - see
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
4) We're a long way from supposing there's a code bug :-)
Mark
On Thu, Dec 13, 2012 at 4:40 PM, Da-Wei Li lida
From your description, why not just write a script to run various
Gromacs programs (MD, analysis, etc)?
dawei
On Tue, Jun 12, 2012 at 2:43 PM, Bao Kai paeanb...@gmail.com wrote:
Hi, all,
I am wondering if Gromacs functions can be called by some other codes.
I know we get some library files
In your own code, you should have a system call function, which can be
used to run any command in your system. Using C as example, you can
write source code like this.
/***/
system(g_rms -s xx.tpr -f xx.trr -o rmsd.xvg);
read in file rmsd.xvg to
Usually /tmp is writable for any user. It looks like this is not a case in
your system. Ask your system administrator.
dawei
On Tue, Oct 11, 2011 at 2:57 PM, Chunxia Gao chunxia@chem.gu.se wrote:
sorry, I wrote it wrong, actually I had added ./configure
--prefix=/home/yourname/... in
hello
Just to share information. My parallel MD run also crash (very rarely) but I
can always bypass the crash point using cpt files.
dawei
On Fri, Aug 12, 2011 at 10:02 AM, Sebastian Breuers
breue...@uni-koeln.dewrote:
Hey,
thank you both for the response. I at least could restart the
It is possible that the terminal that used to run gromacs does not have
GMX_MAXBACKUP set up. if you use some queue software, put export
GMX_MAXBACKUP=0 in the submitting script or even put it into your .bashrc
file.
On Fri, Aug 12, 2011 at 1:53 PM, Hiroshi Fujisaki fujis...@nms.ac.jpwrote:
Dear Mark and others
I did more tests and thought that it might come from numerical error. The
reasons are
1. If I use .trr file instead of the low precision xtc file, things become
better, ie, I get much less snapshots that has high energy.
2. I supplied -pforce in my mdrun -rerun and found
think this is the cause.
best,
dawei
On Thu, Aug 11, 2011 at 8:47 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Da-Wei Li wrote:
Dear Mark and others
I did more tests and thought that it might come from numerical error. The
reasons are
1. If I use .trr file instead of the low precision xtc
type
calculation. The error is just too large.
best,
dawei
On Thu, Aug 11, 2011 at 9:03 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Da-Wei Li wrote:
Dear Justin
An implicit water simulaiton with this short cutoff is problematic but I
think it is fine for rerun. I want to exactly repeat
Hello
Please see my response below.
On Thu, Aug 11, 2011 at 10:23 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 11/08/2011 10:22 PM, Da-Wei Li wrote:
Dear Mark and others
I did more tests and thought that it might come from numerical error. The
reasons are
1. If I use .trr file
Dear Gromacs users:
I recently tried some MM/PBSA stuff using the rerun function of mdrun and
GBSA model. All water molecules are stripped off the trajectory file.
However, when I examine the different energy term, it is disturbing that
short range vdw energy of some snapshot are very high (
, 2011 at 11:12 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 11/08/2011 12:29 AM, Da-Wei Li wrote:
Dear Gromacs users:
I recently tried some MM/PBSA stuff using the rerun function of mdrun and
GBSA model. All water molecules are stripped off the trajectory file.
However, when I examine
at 11:32 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 11/08/2011 1:18 AM, Da-Wei Li wrote:
Dear Mark
That is my thought too.To test this possibility, I created a mdp file
without PBC and use trjconv -pbc nojump to make whole protein. From
visualization in UCSF Chimera, the trajectory
comments about the proposed protocol, force field and water model to
use, will be highly appreciated!
thanks,
Thomas
On 8 June 2011 22:37, Justin A. Lemkul jalem...@vt.edu wrote:
Da-Wei Li wrote:
I really don't think you can get adequate sampling for IDPs that have 40
residues, using full
I really don't think you can get adequate sampling for IDPs that have 40
residues, using full atomic MD.
On Wed, Jun 8, 2011 at 3:25 PM, Michael Daily mdaily.w...@gmail.com wrote:
Do you have some experimental data to compare to your IDP simulations,
like X-ray scattering or some such? I'd
hello
I do not know whether there is an option but you can achieve this easily by
revising top file.
dawei
On Wed, Jun 1, 2011 at 4:59 AM, Kukol, Andreas a.ku...@herts.ac.uk wrote:
Hello,
Is it possible to globally scale all non-bonded interactions by a factor ?
I know there are energy
I remember that 1-4 won't be scaled in the free energy code, right?
dawei
On Wed, Jun 1, 2011 at 3:24 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kukol, Andreas wrote:
Hello,
Is it possible to globally scale all non-bonded interactions by a factor ?
I know there are energy exclusion
Hello, everyone,
Does anyone have experience of doing NVE simulation? I wish to know, for a
system with box size 6.1*6.1*6.1nm, whether the microcanonical ensemble for
a NVE simulation will converge with the canonical ensemble from a NPT
simulation?
Thanks,
--
gmx-users mailing list
Dear all
From Table 5.6 of Gromacs 4.5.4 manu, position restrain constants can be
interpolated in free energy calculations. However, I cannot find how to set
up this. Can somebody help?
thanks.
dawei
--
gmx-users mailing listgmx-users@gromacs.org
hi
It seems that your couple-moltype is missing, that is, no molecules will be
turned off interaction.
dawei
On Thu, Feb 17, 2011 at 8:26 AM, Moeed lecie...@googlemail.com wrote:
Hello Justin
Thanks for your attention. Just to remind you: I am getting blank dgdl and
I found this in log
hello
Now it is almost clear what happened. When couple-intramol is no (default),
all pairwise vdm and charge interaction becomes bonded interaction.
All intra-molecular non-bonded interactions for moleculetype couple-moltype
are replaced by exclusions and explicit pair interactions. In this
Dear users
I tried free energy calculation but grompp couldn't go through. It stops
after
***
Generated 2278 of the 2278 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2278 of the 2278 1-4 parameter combinations
Excluding 3 bonded neighbours
hi,
I did more test and found that it depended on size of the protein. Grompp
will die when number of atoms of the protein is larger than about 200. Is it
possible the source code limit the size of the protein that can be
decoupled?
thanks.
dawei
On Mon, Feb 7, 2011 at 10:34 AM, Da-Wei Li
Well. It actually isn't dead but becomes very slow for large proteins.
dawei
On Mon, Feb 7, 2011 at 11:44 AM, Da-Wei Li lida...@gmail.com wrote:
hi,
I did more test and found that it depended on size of the protein. Grompp
will die when number of atoms of the protein is larger than about
a MD(sd)
with FEP on after the PR?
And are you doing hydration of a protein?
Thank you,
TJ Mustard
On February 7, 2011 at 10:23 AM Justin A. Lemkul jalem...@vt.edu
wrote:
Da-Wei Li wrote:
hello
Here they are the command line and mdp file. I use Gromacs 4.5.3
Minimum cell size due to bonded interactions: 4.960 nm
so that domain decomposition will not work. What is a LJC pair? I did not
see any problem with my system. Everything is fine if free_energy = no.
thanks.
dawei
On Mon, Feb 7, 2011 at 1:38 PM, Da-Wei Li lida...@gmail.com wrote:
hello
My
change these values.
Thank you,
TJ Musard
On February 7, 2011 at 1:08 PM Da-Wei Li lida...@gmail.com wrote:
hi, all
I get another strange error. Once I turn on free energy calculation. mdrun
will complain this:
Initial maximum inter charge-group distances:
two-body bonded
I think you are right.
2010/9/11 wuxiao xiaowu...@hotmail.com:
Dear GMXers,
I have a quad-core computer at hand, on which I would like to install a
parallel implementation of GMX-4.5.1. The homepage
(http://www.gromacs.org/About_Gromacs/Release_Notes/Version_4.5) refers to
running on a
The download link seems wrong on Gromacs webpage. It links to beta4.
dawei
On Wed, Sep 1, 2010 at 4:10 PM, Rossen Apostolov rossen.aposto...@cbr.su.se
wrote:
It is finally here: *Gromacs-4.5* has been just
releasedftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.tar.gz.
All critical issues
Yes it is. Now everything is fine with openmpi instead of mvapich2.
dawei
On Wed, Aug 11, 2010 at 12:59 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
- Original Message -
From: Da-Wei Li lida...@gmail.com
Date: Wednesday, August 11, 2010 6:23
Subject: Re: [gmx-users] New beta
According to our HPC manage, our MVAPICH2's version is 1.0.3.
thanks for the information.
dawei
On Wed, Aug 11, 2010 at 2:52 PM, Roland Schulz rol...@utk.edu wrote:
MVAPICH2 =1.4.1 should be fine. Did you use a version 1.4.1?
On Wed, Aug 11, 2010 at 2:45 PM, Da-Wei Li lida...@gmail.com wrote
Hi,all
Unfortunately, it still crash. Here it is the output of mdrun. Both
Gromacs-4.0.7 and non-parallel 4.5b3 work fine on this system. I use
mvapich2 and intel compiler.
***
Getting Loaded...
Reading file em.tpr, VERSION 4.5-beta3 (single precision)
Loaded with Money
Hello
I tried the Gromacs 4.5 beta. However, my MPI mdrun died. Here it is
the output. The Gromacs-4.0.7 work fine for the same system. It is
protein in water system. There are about 22000 atoms.
***
Will use 9
It will be very little from my experience. Remember that the dominate
part is the non-bonded force calculation.
dawei
On Mon, Jul 19, 2010 at 12:22 PM, ms deviceran...@gmail.com wrote:
Hi,
Do you know where can I find some information on how using tabulated
potential affects gmx performance,
I remember the manu states that it won't cost too much compared with
standard potential function form.
dawei
On Mon, Jul 19, 2010 at 1:22 PM, ms deviceran...@gmail.com wrote:
On 19/07/10 17:32, Da-Wei Li wrote:
It will be very little from my experience. Remember that the dominate
part
You can just delete them in the generated top file.
dawei
On Fri, Jul 16, 2010 at 10:45 AM, C. Batistakis cbat...@yahoo.gr wrote:
Dear all
According to the manual, pdb2gmx generates all the angles, pairs and
dihedrals automatically in a polymer chain. Because I need nothing of them
do you
hi, all
Finally figured out that it was because all numbers in the cmap.itp
file must be separated by only one space,otherwise the program will
read in a zero. I would suggest this to be fixed in the release
version.
have a nice day.
dawei
On Tue, Jun 29, 2010 at 9:05 AM, Da-Wei Li lida
HI, David,
thanks for your advise. I remove the bond angle force and get same
result. It is really strange. If I set +5 on all the 24*24 grid, I
just get a inverted distribution and if I set 0 on all grid, I will
get a uniformed distribution. It is like that 27 regions are force to
have zero cmap
jun 2010 kl. 14.45 skrev Da-Wei Li:
HI, David,
thanks for your advise. I remove the bond angle force and get same
result. It is really strange. If I set +5 on all the 24*24 grid, I
just get a inverted distribution and if I set 0 on all grid, I will
get a uniformed distribution. It is like
Hi, all
I recently download the git version and test the CMAP. However, very
strange result I get. I want to use CMAP support in my own
coarse-grained force field.
Basically, I construct a ALA-ALA-ALA system and turn off all energy
terms except bond length, bond angle and CMAP to do some
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