Hi,
that really depends on your system. There are many ways to set up the same
TI transformation and you are looking for the one that produces the most
easily integrated and non-noisy DVDL-curve for your system. Changing vdw
and eel at the same time can imporve accuracy per CPU effort but that
needs to be tested individually.
You could run several short simulations with different setups and check
which produces the 'best' free energy curve, then invest serious computer
time to converge that one.
What I always try to avoid is adding a charge in one step and removing it
in another, as that seems like an unnecessary large disturbance of your
system.
Thomas
On Sun, December 30, 2012 12:18 am, Nihal Korkmaz wrote:
> 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
>>
>> _______________________________________________
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>
> --
> 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
>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Sun Dec 30 2012 - 06:00:04 PST
