Dear Gromacs user,
I am trying to simulate a protein (nmr structure).I have successfully done
energy minimisation step.Also I have equilibrated the system a 298 k (which
is achieved from 100 ps run) .Now,I am trying to equilibrate the system at
1 bar pressure.After a run of 100 ps ,I am getting
for the tpr file I
get 2 clusters.
Does anybody know why this is the case?
Cheers
Sabine
On 05/10/2013 04:33 PM, Preeti Choudhary wrote:
hello everyone
I am trying to cluster my data using g_cluster.I simulated the whole
protein. I did the g_cluster analysis with only
I am facing problem while using do_dssp.I
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-- Forwarded message --
From: Preeti Choudhary preetichoudhary18111...@gmail.com
Date: Tue, May 14, 2013 at 8:30 PM
Subject: do_dssp
To: Discussion list for GROMACS users gmx-users@gromacs.org
I am facing problem while using do_dssp.I need to store secondary structure
data every
hello everyone
I am trying to cluster my data using g_cluster.I simulated the whole
protein. I did the g_cluster analysis with only certain region of the
protein which I specified using an index file.The program runs fine and
gives 1 cluster.My concern is the warning it gives which states that :-
, Preeti Choudhary
preetichoudhary18111...@gmail.com wrote:
hey this is regarding random seed used in md.this is when it selects the
intial velocity and selects from maxwell-istribution.but is it selects
only
once or selects this random seed every time when grompp makes .tpr
file.really
hey this is regarding random seed used in md.this is when it selects the
intial velocity and selects from maxwell-istribution.but is it selects only
once or selects this random seed every time when grompp makes .tpr
file.really confused about this random seed concept.can u clear my
confusion??
Thankyou
On Wed, Apr 10, 2013 at 11:30 PM, Justin Lemkul jalem...@vt.edu wrote:
On Wed, Apr 10, 2013 at 10:43 AM, Preeti Choudhary
preetichoudhary18111...@gmail.com wrote:
-- Forwarded message --
From: Preeti Choudhary preetichoudhary18111...@gmail.com
Date: Wed, Apr
-- Forwarded message --
From: Preeti Choudhary preetichoudhary18111...@gmail.com
Date: Wed, Apr 10, 2013 at 7:46 PM
Subject: rmsd
To: gmx-users-ow...@gromacs.org
Hi,
I calculated the rmsd of my md simulation trajectory by giving the tpr file
I used as an input in for my final
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