Hi Ram,
-fit rot+trans performs an ordinary least-squares fit using the
reference structure provided with -s, removing rotational and
translational degrees of freedom.
Cheers,
Tsjerk
On Tue, Sep 9, 2008 at 9:47 PM, rams rams [EMAIL PROTECTED] wrote:
Dear Users,
I have a question about the
Hi
I would like to simulate the solutes are embeded in D2O solution.
Could someone explain the difference of simulating D2O solution and H2O
solution?
It differs with FF for D instead of H. It's quite primitive for make
such exchange in topology.
--
Vitaly V. Chaban
School of Chemistry
Dear justin,
I have made the itp file on a basis of chapter 5 of gromacs. Every things
seems fine. my itp file for opls is as follow:
;
[ moleculetype ]
; Name nrexcl
DRG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 opls_185 1 DRG HAD 1
Morteza Khabiri wrote:
Dear justin,
I have made the itp file on a basis of chapter 5 of gromacs. Every things
seems fine. my itp file for opls is as follow:
Seems fine is your own evaluation, but if grompp is giving you errors about an
incorrect topology, then indeed it is not. Did
I have converted .xpm (which generated from *g_hbond) to .eps by using xpm2ps
command, after finished the running of this command showed
There are 1 matrices in .xpm
Matrix 0 is 37501 x 1
Auto tick spacing failed for X-axis, guessing 2
Auto tick spacing for X-axis: major 2, minor 0.4
Auto
minnale wrote:
I have converted .xpm (which generated from *g_hbond) to .eps by using
xpm2ps command, after finished the running of this command showed
There are 1 matrices in .xpm
Matrix 0 is 37501 x 1
Auto tick spacing failed for X-axis, guessing 2
Auto tick spacing for X-axis: major 2,
Dear Justin,
thanks for your help. The last lines of my grompp are:
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4
* Justin A. Lemkul [EMAIL PROTECTED] [2008-09-10 05:46:07 -0400]:
Morteza Khabiri wrote:
Dear justin,
I have made the itp file on a basis of chapter 5 of gromacs. Every things
seems fine. my itp file for opls is as follow:
Seems fine is your own evaluation, but if grompp is giving you
Morteza Khabiri wrote:
Dear Justin,
thanks for your help. The last lines of my grompp are:
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated
I have issued the following command
xpm2s -f .xpm -o .eps
If I mention option -di with m2p it showed
Fatal error:
Library file H_hbond.m2p not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)
Could tell me any suggestion
minnale wrote:
I have issued the following command
xpm2s -f .xpm -o .eps
If I mention option -di with m2p it showed
Fatal error:
Library file H_hbond.m2p not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)
Could tell me
Thanks again Justin for your kind reply
I have given command like this
xpm2ps -f .xpm -o .eps -di .m2p
then it showing the following error
Fatal error:
Library file H_hbond.m2p not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path
minnale wrote:
Thanks again Justin for your kind reply
I have given command like this
xpm2ps -f .xpm -o .eps -di .m2p
then it showing the following error
Fatal error:
Library file H_hbond.m2p not found in current dir nor in default
directories.
(You can set the directories to search with
Hi all,
I had used the tpbconv command to give continuation run on a 2ns
simulation. I had
provided the previois trajectory file, energy file for this. However the
continuation run had
crashed due to power failure and I again had to give a rerun on it.
Everything seems to be
sarbani chattopadhyay wrote:
Hi all,
I had used the tpbconv command to give continuation run on a
2ns simulation. I had
provided the previois trajectory file, energy file for this. However the
continuation run had
crashed due to power failure and I again had to give a rerun on
The post 2ns run had crashed.
The commands were
tpbconv -f 2ns.trr -e 2ns.edr -s 2ns.tpr -extend 1
When it crashed ,the command given was
tpbconv -f ext10ns.trr -s ext10ns.tpr -e ext10ns.edr -o leftrun.tpr
On Wed, 10 Sep 2008 Justin A.Lemkul wrote :
sarbani chattopadhyay wrote:
Hi
sarbani chattopadhyay wrote:
The post 2ns run had crashed.
The commands were
tpbconv -f 2ns.trr -e 2ns.edr -s 2ns.tpr -extend 1
When it crashed ,the command given was
tpbconv -f ext10ns.trr -s ext10ns.tpr -e ext10ns.edr -o leftrun.tpr
So what you're saying then is that the
Am Mittwoch 10 September 2008 13:36:15 schrieb minnale:
Thanks Martin
yes executing of .eps means read out the file.
I am using the following very ugly shell-script to convert to bmp format:
#!/bin/bash
cat $1 | grep -v ^/\* Generated| grep -v ^/\* This| grep -v ^/\* title|
grep -v ^/\*
Hi Tsjerk,
It means the resulting trajectory is free from translational and rotational
degrees of freedom which I can use for the studies of internal dynamics i
suppose.
Ram.
On Wed, Sep 10, 2008 at 3:05 AM, Tsjerk Wassenaar [EMAIL PROTECTED] wrote:
Hi Ram,
-fit rot+trans performs an
vivek sharma wrote:
Hi Everybody,
I am running MD simulation for getting various conformation of a
molecule, that can act as better receptor for docking purpose.
While doing so, I got a number of doubts.
Firstly what should be the range of time step I can keep in .mdp file
(right now I am
It seems that the trajectory is discontinuous. The coordinates in the pdb
file generated
from the trajectory files show that the model corresponding to 2ns in the
2ns.pdb(at the
last ) file is different from the model corresponding to 2ns in the
10ns(extended).pdb( at
the first)
Sarbani
Hi Justin,
Thank you very much for your quick reply It is really encouraging to get
such response
For the answer of third question, How can I assign different random velocity
?
Is it like assigning the different force-field ?
Please elaborate or suggest some reference if you can ?
With
Hi Christian,
Thanks for your idea. I'll start writing up a short manual to make it
available in the QMMM website in the near future. Meanwhile, it will be
great if you and other users can contribute to this manual by writing up
small pieces mentioning the difficulties you faced and how you
Short answer, try Amber99SB with Gaff.
Alan
Message: 1
Date: Fri, 5 Sep 2008 15:06:21 +0200
From: Paula Gonz?lez-Rubio [EMAIL PROTECTED]
Subject: [gmx-users] which force field for a protein-protein complex?
To: gmx-users@gromacs.org
Message-ID:
[EMAIL PROTECTED]
Content-Type:
I'm getting odd behavior with the reference configuration generated by
g_sdf (v. 3.3.3). I am wondering if this is a bug, and if the spatial
density profile is similarly affected.
My test system has simple, regular geometry: a glycine 15-mer held
frozen in a fully extended rod-like
Hi all !
Does anyone have the topology and coordinates of tris-naphthyl-benzene in bulk ?
I would be highly grateful if someone can share those with me.
Thanks a lot in advance.
__
Rohit
Dear users,
The S2 order parameters obtained by using g_chi, are they corresponds to the
Lipari_Szabo NMR order parameters for characterizing the internal motions?
Also it is mentioned in the manual that the obtained S2 parameter
corresponds to a dihedral and the generated plot is residue vs S2.
I was working with protein complex, and after tests some FF, I could obtain
best results with oplss/aa
On Wed, Sep 10, 2008 at 12:07 PM, Alan [EMAIL PROTECTED] wrote:
Short answer, try Amber99SB with Gaff.
Alan
Message: 1
Date: Fri, 5 Sep 2008 15:06:21 +0200
From: Paula Gonz?lez-Rubio
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