[gmx-users] Strange dgdl-value together with lincs

[Berk Hess]

I assume your are using a united atom model.
What are the bonded parameters for the methanol H
in the ethane topology?
Does it have the normal methanol bond and angle potential?
If these parameters are zero, I would indeed expect a spike.

Berk.

> Date: Thu, 14 Feb 2008 18:10:59 +0100
> From: mgoette at mpi-bpc.mpg.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Strange dgdl-value together with lincs
> 
> Hi
> 
> While trying to find, whats wrong with some of my free energy 
> calculation, I stumbled upon a strange thing, I don't understand.
> 
> I'm simulating the interconversion of ethane to methanol in vacuum.
> I'm splitting the process into 3 steps:
> 1. charge of perturbed atoms -> 0
> 2. morph of LJ-parameters and bonds
> 3. charge of perturbed atoms -> B-state values
> 
> Each system is morphed with 1 fs timestep and within 50 steps.
> The total energies at the "borders" of the simulations (qqoff/vdw, 
> vdw/qqon, qqon/vdw and vdw/qqoff) perfectly match and show no jump; the 
> following simulation always got energies and velocities from the one before.
> 
> Now, when running the LJ morph A->B with lincs, the dgdl looks like this:
> http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_lincs_01.png
> For B->A:
> http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_lincs_10.png
> Doing both without lincs yields:
> http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_nolincs_01.png
> For B->A
> http://www.mpibpc.mpg.de/groups/grubmueller/start/people/mgoette/images/dgdl_nolincs_10.png
> 
> I find this spike in the first step extremely strange. Additionally it 
> only occurs, when using shake or lincs as constraint solver. I guess, in 
> a longer process it will contribute to the integral in a neglectable 
> manner, but maybe theres some bug. The latest CVS shows the same behaviour.
> 
> Any comments on that?
> 
> Regards
> 
> -- 
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>          mgoette2[at]gwdg.de
> WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/