Hi,
I just want to add what worked for me to close this thread properly.
My initial structures were 'very tense' so i decided to strip water and
ions and run minimization in vacuum for few hundred steps.
Then i added solvent and ions and ran a short minimization with SHAKE to
relax the water and ions while holding the rest of the system fixed.
now molecular dynamics is running happily.
Many Thanks,
Taufik
Bill Ross wrote:
>> but can i do something about this, for example open the
>> prmtop file or the inpcrd file and 'somehow' find atom 4615 and change
>> its position?
>
> Technically you could do the math to figure out which numbers
> in the inpcrd to change (consider each atom has x, y, z coords).
> Or you could generate a pdb and look at it to actually understand
> what the problem is, posssibly fixing it and regenerating prmtop
> and inpcrd.
>
> What I'd be inclined to try is some 10K dynamics (with SHAKE)
> to see if that will get you over the problem. You might even
> go on to start your equilibration from there.
>
> Bill
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 24 2010 - 13:00:02 PDT
