Hi Tommaso,
> First minimization
> &cntrl
> imin = 1,
> maxcyc = 3500,
> ncyc = 1500,
> ntb = 1,
> ntr = 0,
> cut = 15
> /
You don't need a cut of 15 here since you have PME. 8 will do.
> Did I miss something?
> Now I try to set the simulation with ntp=1, since I missed it.
ntp=1 is the default so that won't help.
> I built the initial structure with the utility packmol. I don't know
> other methods in order to set the initial system, because, if I use
> the solvatebox command of tleap with my box of PG molecules, I obtain
> a box which is too large with a huge number of water molecules (>
> 190,000).
The starting structure is almost certainly your problem. Try setting ntpr=1
and maxcyc=10. Then see which atom is reported to have the highest force on
it and go take a look at that atom in your starting structure. Posting your
output from this run will also aid people helping you.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Tue Jan 25 2011 - 09:30:06 PST
