[gmx-users] Flat-bottom potential SEGFAULT

[Erik Marklund]

> On 28 Mar 2016, at 01:52, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 3/26/16 12:47 PM, Erik Marklund wrote:
>> Dear dynamicists,
>> 
>> I am using flat bottom potentials to prevent water molecules from evaporating from a droplet in vacuum. The manual suggests this is pretty straightforward, but we run into a segfault with our approach. Having never used flat-bottom potentials before, chances are we are doing something wrong without realising it. Let me describe what we do and perhaps you can tell me where things go wrong.
>> 
>> We make our own copy of tip3p.itp, in which we put a [ position_restraints ] directive for the OW1, HW2, and HW3 atoms:
>> [ position_restraints ]
>> ; id func_type    g   r  k
>> 1    2            1   10 1000
>> 2    2            1   10 1000
>> 3    2            1   10 1000
>> 
>> We then create a new gro-file, where we move all water atoms in the middle of the box. This is to be used for reference coordinates in the next step.
>> 
>> We run grompp, where we provide the new gro file using the -r flag.
>> 
>> We launch mdrun, which segfaults. If we prepare the system without the -r flag in the previous step everything runs fins, but the reference point for the flat-bottom potential is presumably wrong.
>> 
>> Where might the error be?
>> 
> 
> I just did this with a toy system of a single water molecule and it worked quite well.  What version of GROMACS are you using?  Does a simple test like I did work?
> 
> -Justin

Hi,

Forgot to mention the version. It is 5.1.1. Will run some simple tests like yours and get back with more info.

Kind regards,
Erik

> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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