- Original Message -
From: sonali dhindwal sonali11dhind...@yahoo.co.in
Date: Friday, May 21, 2010 15:38
Subject: Re: [gmx-users] enegry minimisation
To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org
: Re: [gmx-users] enegry minimisation
To: sonali dhindwal sonali11dhind...@yahoo.co.in
Date: Wednesday, 19 May, 2010, 8:39 PM
For position restraints you need to do the following:
1. define a name.itp file which looks like:
; In this topology include file, you will find position restraint
Subject: Re: [gmx-users] enegry minimisation
To: sonali dhindwal sonali11dhind...@yahoo.co.in
Date: Wednesday, 19 May, 2010, 8:39 PM
For position restraints you need to do the following:
1. define a name.itp file which looks like:
; In this topology include file, you will find
sufficient to restrain the
structure.
-Justin
Thanks in advance.
--
Sonali Dhindwal
--- On *Wed, 19/5/10, Gaurav Goel /gauravgoel...@gmail.com/* wrote:
From: Gaurav Goel gauravgoel...@gmail.com
Subject: Re: [gmx-users] enegry minimisation
To: sonali dhindwal sonali11dhind
:
From: Gaurav Goel gauravgoel...@gmail.com
Subject: Re: [gmx-users] enegry minimisation
To: sonali dhindwal sonali11dhind...@yahoo.co.in
Date: Wednesday, 19 May, 2010, 8:39 PM
For position restraints you need to do the following:
1. define a name.itp file which looks like
...@gmail.com
Subject: Re: [gmx-users] enegry minimisation
To: jalem...@vt.edu, Discussion list for GROMACS users
gmx-users@gromacs.org
Date: Thursday, 20 May, 2010, 5:36 PM
Can you try using g_rms to compare the difference between the
structures before and after EM.
-Gaurav
A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] enegry minimisation
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Thursday, 20 May, 2010, 6:46 PM
sonali dhindwal wrote:
Hello Gaurav,
when i did g_rms with structre before energy minimisation
hello Jusitn,
Thanks for your reply,,
I am sending you the link,
so that you can see the changes in the protein, I have specifically
shown that part of the protein, where I am seeing changes,
http://picasaweb.google.co.in/sonali11dhindwal/Protein?feat=directlink
Yello
beeta sheets are of the
sonali dhindwal wrote:
Hello All
This question may sound trivial to many, but as i am new to this field,
please help.
I want to ask a question regarding my previous query of distortion of
protein strucutre after molecular dynamcs simulation.
Can you provide a link to your previous post,
sonali dhindwal skrev:
Hello All
This question may sound trivial to many, but as i am new to this
field, please help.
I want to ask a question regarding my previous query of distortion of
protein strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using
sonali dhindwal skrev:
Hello All
This question may sound trivial to many, but as i am new to this
field, please help.
I want to ask a question regarding my previous query of distortion of
protein strucutre after molecular dynamcs simulation.
I have noticed that after enegry minimisation using
: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] enegry minimisation
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Wednesday, 19 May, 2010, 5:17 PM
sonali dhindwal wrote:
Hello All
This question may sound trivial to many, but as i am new to this field,
please help.
I
, 19/5/10, Justin A. Lemkul /jalem...@vt.edu/* wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] enegry minimisation
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Wednesday, 19 May, 2010, 5:17 PM
sonali dhindwal wrote:
Hello All
--- On Wed, 19/5/10, Erik Marklund er...@xray.bmc.uu.se wrote:
From: Erik Marklund er...@xray.bmc.uu.se
Subject: Re: [gmx-users] enegry minimisation
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Wednesday, 19 May, 2010, 5:31 PM
sonali dhindwal skrev:
Hello All
This question may
stuff
;
emtol = 1000.0
emstep = 0.01
I hope it will help you to guide me further
Thanks
--
Sonali Dhindwal
--- On *Wed, 19/5/10, Erik Marklund er...@xray.bmc.uu.se* wrote:
From: Erik Marklund er...@xray.bmc.uu.se
Subject: Re: [gmx-users] enegry minimisation
:
From: Erik Marklund er...@xray.bmc.uu.se
mailto:er...@xray.bmc.uu.se
Subject: Re: [gmx-users] enegry minimisation
To: Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
Date: Wednesday, 19 May, 2010, 5:31 PM
sonali
further
Thanks
--
Sonali Dhindwal
--- On *Wed, 19/5/10, Erik Marklund /er...@xray.bmc.uu.se
mailto:er...@xray.bmc.uu.se/* wrote:
From: Erik Marklund er...@xray.bmc.uu.se
mailto:er...@xray.bmc.uu.se
Subject: Re: [gmx-users] enegry minimisation
--- On Wed, 19/5/10, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] enegry minimisation
To: Gromacs Users' List gmx-users@gromacs.org
Date: Wednesday, 19 May, 2010, 5:45 PM
sonali dhindwal wrote:
Thanks Justin for your reply.
Yes I have
/jalem...@vt.edu/* wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] enegry minimisation
To: Gromacs Users' List gmx-users@gromacs.org
Date: Wednesday, 19 May, 2010, 5:45 PM
sonali dhindwal wrote:
Thanks Justin for your reply.
Yes I have
I seem to say this several times per week: in my experience (and in
the
experience of many others who have posted here) the charges and charge
groups output by PRODRG are often unsatisfactory, requiring manual
Might be an idea then to put the comments on the PRODRG page on the
GROMACS website
Dallas B. Warren wrote:
I seem to say this several times per week: in my experience (and in
the
experience of many others who have posted here) the charges and charge
groups output by PRODRG are often unsatisfactory, requiring manual
Might be an idea then to put the comments on the PRODRG
21 matches
Mail list logo
