Re: [gmx-users] Peptide aggregation

2008-09-20 Thread Ran Friedman, Biochemisches Inst. 

Dear Leon,

Note that you can already use g_clustsize to check the aggregates. I'll 
contact you off list next week with the modified version.


Ran

On Fri, 19 Sep 2008 17:13:02 +0100
 Léon Salgado [EMAIL PROTECTED] wrote:

Dear Dr. Ran Friedman

Would you please be so kind to send me your version, to calculate then the 
rgyr of the largest aggregate.
The box was built with a layer of 1.2 nm around the solute (editconf -d 
1.2).


Leon

Ran Friedman wrote:

Dear Leon,

You can try to use g_clustsize to get the aggregates. I have a version
that can calculate the gyration radius of the largest aggregate, but
this would work only if your box is big enough and I haven't tried it
with rhombic dodecahedron boxes.

Ran.

Léon Salgado wrote:
  

Dear gmx users

I did some simulations of multimers (peptides) in rhombic dodecahedron
boxes. In the initial configuration of the system, the peptides are
close of each other in the center of the box.

My aim to see if the peptides do aggregate during the trajectory or if
they tend to stay apart. A rough estimate can be taken from the
gyration radius for all the peptides together.

Already did a trjconv -pbc nojump pre-treatment on the trajectory,
before calculating the Rgyr. The gyration.xvg plots sometimes do show
abrupt jumps, and this is surely due to boundary effects, if I
correctly understood the PBC idea. If a peptide approaches the
boundary, it appears on the opposite side, thus rgyr will show a false
sudden increase. In fact, the peptide could be closer to the rest of
the other peptide molecule(s).

Thus my question is:
how to deal with peptide clusters that span over the periodic boundaries?

A similar question was done by Singh:
http://www.gromacs.org/pipermail/gmx-users/2007-January/025474.html

and it  was suggested by Chris Neale to pre-process the trajectory
(see
http://www.gromacs.org/pipermail/gmx-users/2007-January/025481.html)
with:

trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump

but I'm getting infinite loops on the -pbc cluster treatment, same as
reported by Chris
(http://www.gromacs.org/pipermail/gmx-users/2008-July/035343.html).

Best,
Léon

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--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Institute of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Skype: ran.friedman
--

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Re: [gmx-users] RE: Time step in md

2008-09-20 Thread Omer Markovitch 
On Sat, Sep 20, 2008 at 10:29, Vitaly Chaban [EMAIL PROTECTED]wrote:

  could you explain my the secret of choosing to time step for md
  integrator?



The secret is, to have the timestep small enough so that you could truly
say between two consecutive steps the forces are linear, and to have it
large enough so the computation would be feasible.

Other then that, look at the previous answers you got for a more hands on
approach. You might also want to read about integrating MD.
--Omer Markovitch.
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[gmx-users] DMSO-protein simulation

2008-09-20 Thread prasun kumar 
Dear Users,

I am trying to do a DMSO-protein simulation.As I have posted this query
earlier also and got one suggestion of adding atomtypes section in dmso.itp
file that is not present in it.The problem I am facing here is:

 how to calculate c6  c12 coloumn for DMSO
thanx in advance

-- 
PRASUN (ASHOKA)
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