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

[Rama Gullapalli]

yes that is what it will exactly do....you can also
specify the timeframe of the output...
Regards
Rama

--- Samuel Flores <samuel.flores at yale.edu> wrote:

> 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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