[gmx-users] How can I reconstruct the system in CGMD simulation?

rasoul nasiri nasiri1355 at gmail.com
Thu Dec 17 15:25:16 CET 2009


My purpose is finding of denaturation mechanism of proteins with MArtini
CGFF by Gromacs.
I mean after filling box in which there are beads of protein from water
beads with suitable van der wall distance (larger than 0.105nm), when I want
to start production phase, first switch back to the smaller radius of van
der waals of the water beads, then I will continue CGMD simulation. Is it
possible I reduce this radius? Which commands of Gromacs suit can do it?


On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> rasoul nasiri wrote:
>> greetings GMX users,
>> When I use genbox command for filling solvent in CGMD simulation with
>> Gromacs suit, I must use a larger van der Waals distance to avoid crashes.
>> when I use default value (0.105nm), system will crash. Which distance is
>> suitable for performing CGMD simulation. I used  0.15 or 0.2nm as distances.
>> Are those OK?
> Read up on your forcefield and find out how "large" the particles tend to
> be. It only has to be good enough, not perfect.
>  I have to switch back to the smaller radius afterward, Is it correct?
> Changing what for what purpose?
>  if yes, How can I do it? I tried with editconf but could not.
> I don't know what you mean.
> Mark
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