Dr Steinbrecher,
I checked the input files and I am using the soft-core parameter, ifsc = 1.
Here is my input file for
V0:
NPT production
&cntrl
imin = 0, ntx = 5, irest = 1,
ntpr = 10000, ntwr = 100000, ntwx = 10000,
ntf = 1, ntc = 1,
ntb = 2, cut = 10.0,
nstlim = 500000, dt = 0.001,
temp0 = 300.0, ntt = 3, gamma_ln = 2,
ntr = 1, restraint_wt = 25.0,
restraintmask = ':1-2'
ntp = 1, pres0 = 1.0, taup = 2.0,
icfe=1, clambda = 0.99,
ifsc=1,
crgmask=':1-2',
scmask=':1-2',
&end
Residues 1 and 2 happen to be K+ and Cl-.
For V1:
NPT production
&cntrl
imin = 0, ntx = 5, irest = 1,
ntpr = 10000, ntwr = 100000, ntwx = 10000,
ntf = 1, ntc = 1,
ntb = 2, cut = 10.0,
nstlim = 500000, dt = 0.001,
temp0 = 300.0, ntt = 3, gamma_ln = 2,
ntp = 1, pres0 = 1.0, taup = 2.0,
icfe=1, clambda = 0.99,
ifsc=1,
crgmask='',
scmask='',
&end
Regarsd
Sai
On Wed, Jan 18, 2012 at 12:15 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > The Coulomb part is smooth, but when I come to the vander Waals part at
> > lambda = 0.96. 0.97, 0.98, 0.99, the deviations of dV/dL are really very
> > large and the associated rms in dV/dL is large too.
> > Below are the values pasted from my step2 (removal of VdW) for KCl in
> > water.
> >
> > lambda dV/dL rms
>
> > 0.96 -45.3181 25.7754
> > 0.97 -60.0310 34.3345
> > 0.98 -89.1323 51.1157
> > 0.99 -177.6619 106.7890
>
> Are you sure you are using softcore potentials on all disappearing atoms?
> This looks like the origin singularity problem that Sc should fix. Check
> your input files to see if ifsc etc. are really all set ok.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Wed Jan 18 2012 - 11:00:04 PST
