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

[Justin A. Lemkul]

K. Singhal wrote:
> Hi
> 
> 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".
> 

Points 2 and 3 indicate that whatever simulations you're trying to perform are 
simply unstable.  If they don't crash immediately, they're giving meaningless 
output, right?

> 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. 
> 

Do you get the same effects if you run a "normal" simulation on CPU and not GPU? 
  That information would be critical for properly diagnosing what's going on. 
If it's not GPU-specific, in all likelihood whatever you're doing is incorrect 
somewhere along the way.

-Justin

> Thanks & Regards
> Kush
>  
> 
> 
> -----------------------------------------------------------------------------------
> *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 <mailto:k.singhal at uva.nl>
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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