[gmx-users] Re: Secondary structure loss in implicit solvent simulations

K. Singhal k.singhal at uva.nl
Mon Jan 24 13:20:36 CET 2011


1) I am using Amber03 forcefield.

2) In most cases Yes, but in others, implicit solvent simulations tend to crash almost immediately (after reporting segmentation fault).

3) It generally takes less than a couple of 100 ps for the loss of the secondary structure. A few times, I even received .gro files at the end with all values as "nan".

Earlier I thought it might be a problem with equilibration, but I have tried to run energy-minimization more than once followed by position-restrained runs as well (to equilibrate H-atoms). But the end result hasn't changed. 

Thanks & Regards

Michael Shirts:
A few questions:

1) What force field are you using?
2) do you get the same answers with and without GPU acceleration?
3) How long does it take for secondary structure to disappear?  100's
of ps?  10's of ns?

Kushagra Singhal
Promovendus, Computational Chemistry
van 't Hoff Institute of Molecular Sciences
Science Park 904, room C2.119
1098 XH Amsterdam, The Netherlands
+31 205256965
Universiteit van Amsterdam
k.singhal at uva.nl

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