[gmx-users] pdb file from last frame of mdrun?

[Samuel Flores]

Hi guys,
 
If I want a pdb file from the last frame of an mdrun, is it as simple as
putting a -c output.pdb after the mdrun command?  Will gromacs understand
that I want a pdb rather than .gro output?

Sam


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Mu Yuguang (Dr)
Sent: Sunday, October 02, 2005 9:21 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] Discrepancy between Free Energy
PerturbationusingGromos96 and OPLS

Dear Sandeep,
Although I have done the work as you did. But from the quite different
partial charges set used by the two force fields, it is not surprised to
have such different results. Usually the free energy calculation depends
on charges greatly.
The more important thing is to check your convergence of your simulation
to validate your results.

Dr. Yuguang Mu
Division of Structural and Computational Biology
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive 
Singapore 637551
Tel: 63162885
Fax: 67913856
 
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Sandeep Somani
Sent: Saturday, October 01, 2005 1:12 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Discrepancy between Free Energy Perturbation
usingGromos96 and OPLS

hi all 

I did a Slow Growth (dummy -> real) based FEP of a small ligand bound to
a protein using Gromos and OPLS ff. 
Description of ligand in both cases is identical. 

Free energy change from the Gromos simulation is reasonable but the
number from OPLS is an order of magnitude more negative. 

All parameters (reaction field electrostatics, constraints in topology,
delta-lambda etc) other than the ff are identical. Am using gmx3.2.1.

Has anyone encountered this before ? what could be the origin of this
discrepancy ? 

Thanks and Regards
Sandeep 

---
Research Associate
Computational Biology Group
Bioinformatics Institute
Singapore

http://web.bii.a-star.edu.sg/~ssomani/








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