Would the accuracy be enhanced if I treat vdW and electrostatics
separately -by turn off the charges manually etc- during equilibration?
Thanks,
Elif
On 12/29/2012 6:59 AM, steinbrt.rci.rutgers.edu wrote:
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
E. Nihal Korkmaz
Research & Teaching Assistant
UW-Madison, Biophysics Program
Member of Qiang Cui Lab
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644,
Email: korkmaz.wisc.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Dec 29 2012 - 21:30:03 PST
