As the manual states, if you're just doing minimization to remove contacts,
it should be ok to just use ntc = ntf = 2. Others might be qualified to
comment, but I believe that two things the minimizer does not do well with
are 1) rigid water molecules and 2) periodic boundary conditions. In those
cases especially, the minimizer can pretty much only be used as a practical
tool for removing bad contacts.
Brian
On Wed, Mar 6, 2013 at 10:32 AM, 강현아 <hakang.postech.ac.kr> wrote:
> Thank you for your reply.
>
> Actually, I am using ntc and ntf = 2 in equilibration and regular MD of
> rigid water model.
> But, in energy minimization, I have used ntc and ntf = 1... because of the
> information in AMBER 11 manual.
>
> According to the AMBER 11 manual (p. 32, ntc option),
> "Since SHAKE is an algorithm based on dynamics, the minimizer is not aware
> of what SHAKE is doing;
> for this reason, minimizations generally should be carried out without
> SHAKE.
> One exception is short minimization whose purpose is remove bad contact
> before dynamics begin."
>
> I just want to minimize the energy of TIP5P water periodic box.
> For this, ntc and ntf = 2 is more reasonable?
> Frankly, I am not sure... what is better.
> I will try it first.
> Thanks again.
>
>
> Best regards,
> Hyeona Kang
>
> -----Original Message-----
> From: Brian Radak [mailto:radak004.umn.edu]
> Sent: Wednesday, March 06, 2013 11:35 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] TIP5P water simulation
>
> I have no experience with TIP5P, but don't you have to set ntc and ntf = 2
> for rigid water systems?
>
> Regards,
> Brian
>
> On Wed, Mar 6, 2013 at 6:31 AM, 강현아 <hakang.postech.ac.kr> wrote:
>
> > Hello,
> >
> >
> >
> > Now I am doing TIP5P water simulation.
> >
> >
> >
> > Unlike TIP3P and TIP4P water simulation, in TIP5P water simulation,
> > make some troubles.
> >
> >
> >
> > I have followed below procedure.
> >
> >
> >
> > 1) In xleap
> >
> >
> >
> > source leaprc.ff99SB
> >
> > loadAmberParams frcmod.tip5p
> >
> > solvateBox TP5 TP5 12 0.75
> >
> > saveAmberParm TP5 tip5p.prmtop tip5p.inpcrd
> >
> >
> >
> > ð Obtain tip5p.prmtop and tip5p.inpcrd files
> >
> >
> >
> > 2) Energy minimization
> >
> >
> >
> > mdin file
> >
> >
> >
> > &cntrl
> >
> > igb = 0,
> >
> > dielc = 1.0,
> >
> > ntx = 1,
> >
> > irest = 0,
> >
> > ntb = 1,
> >
> > ntp = 0,
> >
> > temp0 = 300.0,
> >
> > ntf = 1,
> >
> > ntc = 1,
> >
> > tol = 0.0005,
> >
> > cut = 8.0,
> >
> > ibelly = 0,
> >
> > dt = 0.002,
> >
> > maxcyc = 25000,
> >
> > imin = 1,
> >
> > ntmin = 2,
> >
> > ntpr = 1,
> >
> > ntwx = 0,
> >
> > ntt = 1,
> >
> > ntr = 0,
> >
> > /Hold the sugar fixed
> >
> > 5.0
> >
> > RES 1
> >
> > &END
> >
> > &end
> >
> >
> >
> > &ewald
> >
> > nfft1 = 48, nfft2 = 48, nfft3 = 36,
> >
> > order = 4, ischrgd = 0, verbose = 0, ew_type = 0,
> >
> > dsum_tol = 0.00001, netfrc = 1, skinnb = 1.0,
> >
> > &end
> >
> >
> >
> > After energy minimization with above mdin file, generated mdinfo file
> > is very strange.
> >
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> >
> > 25000 -7.9681E+06 4.5491E+10 2.2031E+12 O 1
> >
> >
> >
> > BOND = 230.2710 ANGLE = 0.0000 DIHED =
> > 0.0000
> >
> > VDWAALS = -171.2044 EEL = -7968132.9306 HBOND =
> > 0.0000
> >
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 0.0000
> >
> >
> >
> > RMS and GMAX values seem to diverge.
> >
> >
> >
> > I cannot find what is the problem with above procedure.
> >
> > Please help me.
> >
> >
> >
> > Thanks in advance.
> >
> >
> >
> >
> >
> > Best regards,
> >
> > Hyeona Kang
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute
> appropriate address.
> _______________________________________________
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>
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>
>
>
> _______________________________________________
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Wed Mar 06 2013 - 11:00:02 PST
