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
>
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> 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
====================================================================
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Received on Wed Mar 06 2013 - 07:00:03 PST
