Hi, Elif,
it is quite possible to have large DVDL values at some lambdas, especially
when many charges are changed, the curves can be very steep. This will
negatively impact your numerical integration accuracy, but is not
necessarily a sign of some bigger problem.
Thomas
On Fri, December 28, 2012 6:46 pm, Nihal Korkmaz wrote:
> Dear all,
>
> I am trying to get the free energy caused by 2 arginine mutations in a
> 60 residue protein. To have more control over the course of simulation I
> am following a 3 step procedure as described in the tutorial 9. My
> question is about the charge removal part, I am removing the charges on
> the whole softcore region which is composed of side chains of the 2
> arginines and the 2 counter ions that are not present in mutant system
> (V1). Is it normal to have large DV/DL numbers like this?
>
> Etot = -44404.9050 EKtot = 11028.0591 EPtot = -55432.9641
> BOND = 169.7565 ANGLE = 456.8468 DIHED =
> 631.1784
> 1-4 NB = 215.1196 1-4 EEL = 1808.0657 VDWAALS =
> 7920.2721
> EELEC = -66634.2033 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> DV/DL = 464.5739
> EKCMT = 5164.4127 VIRIAL = 5044.5572 VOLUME =
> 363040.4469
> Density =
> 0.5075
> Ewald error estimate: 0.1197E-03
>
> mdin:
> NPT production
> &cntrl
> imin = 0, ntx = 5, irest = 1,
> ntpr = 1000000, ntwr = 100000, ntwx = 10000,
> ntf = 1, ntc = 2, noshakemask=':64,65,23,43 & !
> (.CA,C,N,O,H,H1,H2)',
> ntb = 2, cut = 12.0,
> nstlim = 100000, dt = 0.001,
> temp0 = 300.0, ntt = 3, gamma_ln = 20,
> ntp = 1, pres0 = 1.0, taup = 2.0,
> icfe=1, clambda = 0.1,
> ifsc=0,
> crgmask='',
> &end
>
>
> Thank you in advance,
> Elif
>
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>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Sat Dec 29 2012 - 05:30:02 PST
