Dear All,
I was working previously with the Amber4.1 to run dynamics of peptides in a box of water. Recently we got the new version of Amber7. In comparison to Amber 4.1, new parameters are added and some have been eliminated like imgslt, nrun, idiel, init, ndfmi...
For dynamics in a box of water (generated with WATBOX216) with periodic condition I was using the following parameters file md0.in with a heating period of 20ps with amber4.1:
MD0 Peptide BoxWater
&cntrl
imin = 0, nmrmax = 1,
ntx = 1, irest=0,
ntxo = 1, ntpr = 1000, ntwx = 1000, ntwe = 1000,ntwprt = -1,
ntf = 1, ntb = 2, idiel = 1, cut = 12.0, nsnb = 10, scee = 1.2,
ibelly = 0, ntr = 0,
nrun = 1, nstlim = 200000, ndfmin = 6, nscm=1000,
init = 3, t = 0, dt = 0.001,tautp = 0.2,
temp0 = 300.0, tempi = 10.0, ntt = 5, vlimit = 20.0,
ntp = 1, pres0 = 1.0, comp = 44.6, taup = 0.2, npscal = 1,
ntc = 1,
imgslt = 0,
&end
#Heating
&wt type='TEMP0', istep1=1, istep2=20000,
value1=10.0, value2=300.0, &end
&wt type='TEMP0', istep1=20001, istep2=200000,
value1=300.0, value2=300.0, &end
&wt type='END' &end
&rst iat=0 &end
With this parameters in amber4.1, during the dynamics the total energy increased during the heating period and then was relatively stable.
Now with Amber7 I'm using the following md0.in parameter file:
MD0 Peptide BoxWater
&cntrl
imin = 0, nmropt = 1,
ntx = 1, irest=0,
ntxo = 1, ntpr = 1000, ntwx = 1000, ntwe = 1000, ntwprt = 388,
iwrap=1,
ntf = 1, ntb = 2, cut = 12.0, nsnb = 10, scee = 1.2,
ibelly = 0, ntr = 0,
nstlim = 200000, nscm=1000,
t = 0, dt = 0.001,tautp = 0.2,
temp0 = 300.0, tempi = 10.0, ntt = 1, vlimit = 20.0,
ntp = 1, pres0 = 1.0, comp = 44.6, taup = 0.2, npscal = 1,
ntc = 1,
&end
#Heating
&wt type='TEMP0', istep1=1, istep2=20000,
value1=10.0, value2=300.0, &end
&wt type='TEMP0', istep1=20001, istep2=200000,
value1=300.0, value2=300.0, &end
&wt type='END' &end
&rst iat=0 &end
In this case, with amber7, during the dynamics the energy increased during the heating period like previously and then decreased progressively during the rest of the dynamics, the decreasing is higher during the 100ps following the heating period. I verified the temperature and it is constant during the all dynamics after 20ps.
Does someone has observed this problem already, is it due to my water box equilibration or to some new parameters defined as defaults that I did not specify correctly?
Thanks in advance for your help
Best regards
Florence Casset
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Florence Casset Synt:em
Parc Scientifique G.Besse
Computational Drug Discovery 30000 Nimes
email: fcasset_at_syntem.com France
Tel: +33 (0)4 66 04 86 66 Fax: +33 (0)4 66 04 86 67
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Received on Wed May 15 2002 - 02:48:23 PDT
