Hi Yunjie,
You cannot do this with Sander and I'm not sure why you'd want to. In fact
I'm not sure why you think an electrostatic cutoff in GB is warrantied at
all - especially one as small as 9 angstroms...
What do you hope to gain by having a second even smaller vdw cutoff? You
still need to generate a pair list and loop over atoms so it is unlikely to
save you much if anything at all. PMEMD supports dual cutoffs for periodic
boundary simulations, where potentially it can make sense but I do not think
it supports this for GB. You could hack it into egb.f yourself fairly easily
but I don't see why you'd want to do that unless you wanted to experiment
with EEL / VDW effects as a function of cut off distance.
In my opinion (others may differ here) if you are NOT doing periodic
boundary simulations with PME (such as GB) then you should NOT use any form
of cutoff... period!
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Yunjie Zhao
> Sent: Sunday, May 03, 2009 8:53 PM
> To: AMBER.ambermd.org
> Subject: [AMBER] problem with cutoff
>
> Dear Amber users,
>
> Using Amber 9, I am trying to do molecular simulations with GB
> implicit
> solvent model. I have done a cut-off to distinguish short-range and
> long-range interactions. Now I am trying to distinguish the vdw and
> electrostatic interactions, such as cutoff of vdw with 6 angstrom and
> cutoff of electrostatic with 9 angstrom. How can I do this? Can anyone
> tell
> me how to write the input file?
>
> My input file:
> MD Generalised Born simulation
> &cntrl
> imin = 0, ntb =0,
> igb = 1, ntpr = 10000, ntwx = 10000,
> ntt = 3,gamma_ln = 1.0,
> tempi = 300.0, temp0 = 300.0,
> nstlim = 10000000, dt = 0.001,
> cut = 9
> /
>
> Thanks!
> _______________________________________________
> 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 May 20 2009 - 14:24:45 PDT
