[gmx-users] Restart files

Anton Feenstra feenstra at few.vu.nl
Tue Aug 30 08:30:34 CEST 2005

David van der Spoel wrote:

> On Sat, 2005-08-27 at 13:03 -0400, Bob Johnson wrote:
>>Hello everyone,
>>My system involves an infinite nanotube, a single stranded DNA molecule, and
>>some water. After performing several simulations, the DNA molecule drifts along
>>the nanotube and half of the DNA ends up in the next periodic box. Now I want to
>>add additional water molecules (or methanol molecules) to the system. When I add
>>just one water molecule, it seems that the simulation loses memory of the fact
>>that the DNA on one side of the box is bonded to the DNA on the other side.
>>Normally when the DNA slides into the next periodic box, VMD will draw long
>>bonds stretching across the nanotube connecting the truncated DNA molecule with
>>the portion that now appears on the opposite side of the box. However, upon
>>addition of one water molecule, no bonds are drawn. It seems that the
>>simulation now treats the DNA as two truncated pieces instead of realizing that
>>they are, in fact, bonded together. Eventually the simulation crashes. All I am
>>doing is adding one extra water to the topology file like so,
> You never say how you add the water. You should definitely not edit your
> box size in the direction of the DNA/Tube.

Also you should not assume that VMD interprets your system in the same 
way that Gromacs does, i.c., Gromacs may still consider the DNA on 
'opposite' sides of the periodic box bonded, while VMD does not.



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|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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