Dear sir ,
I am doing lipid simulation work using lipid force field of
amber14.I am not getting a idea that how we can analyse our simulation
result using amber software.please if possible then tell me some related
link with analysis part and tutorials.
Thanking you
Vishnudatt Pandey
On Sat, Oct 10, 2015 at 9:56 AM, David A Case <
dacase.scarletmail.rutgers.edu> wrote:
> On Fri, Oct 09, 2015, Vu Truong wrote:
> >
> > Thanks for your response. Yes, I do have nitrogen molecules in my system
> > which is non-standard residues. So do you think if the cut-off distance
> may
> > also be the reason for that error?
>
> There is no reason, per se, that N2 molecules should cause problems, but
> double-check the Lennard-Jones and bond parameters you are using. Try a
> short
> simulations without the N2 to see if the vlimit messages go away. Look for
> short contacts between the N2 and other atoms in the system.
>
> ...good luck....dac
>
>
> _______________________________________________
> 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 Nov 18 2015 - 02:00:06 PST
