Hi Anita,
You should at least be using irest=1 and ntx=5 after the first stage,
since you would want to restart using the coordinates and velocities from
the previous run. Currently, you are basically starting a new simulation
(generating random velocities) at each stage, which is quite likely the
reason for fluctuations at the start of each run.
Best,
------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC LCBC
BCH 4108
CH - 1015 Lausanne
------------------------------------------------------
On 10/13/15, 07:06, "Anitha Jagadesh" <anitha_jagadesh.yahoo.com> wrote:
>Dear all
>
>I have run MD-heating step for a drug-protein complex system (0-300 k),
>but at the end of run, the drug has moved substantially. In order to
>verify the results, I have re-run the heating in stages. The six stage
>inputs are as follows:
>Heat 1:
>Explicit solvent initial heating mdin
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=1000, ntwx=1000, nstlim=200000,
> dt=0.002, ntt=3, gamma_ln=5.0, ig=-1,
> ntc=2, ntf=2, cut=8, ntb=1,
> iwrap=1, ioutfm=1, nmropt=1,
> tempi = 0.0, temp0 = 50.0
> /
> &wt
> TYPE='TEMP0', ISTEP1=0, ISTEP2=150000,
> VALUE1=10.0, VALUE2=50.0,
> /
> &wt TYPE='END' /
>Heat 2
>Explicit solvent initial heating mdin
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=1000, ntwx=1000, nstlim=200000,
> dt=0.002, ntt=3, gamma_ln=5.0, ig=-1,
> ntc=2, ntf=2, cut=8, ntb=1,
> iwrap=1, ioutfm=1, nmropt=1,
> tempi = 50.0, temp0 = 100.0
> /
> &wt
> TYPE='TEMP0', ISTEP1=0, ISTEP2=150000,
> VALUE1=60.0, VALUE2=100.0,
> /
> &wt TYPE='END' /
>Heat 3
>Explicit solvent initial heating mdin
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=1000, ntwx=1000, nstlim=200000,
> dt=0.002, ntt=3, gamma_ln=5.0, ig=-1,
> ntc=2, ntf=2, cut=8, ntb=1,
> iwrap=1, ioutfm=1, nmropt=1,
> tempi = 100.0, temp0 = 150.0
> /
> &wt
> TYPE='TEMP0', ISTEP1=0, ISTEP2=150000,
> VALUE1=110.0, VALUE2=150.0,
> /
> &wt TYPE='END' /
>Heat 4
>Explicit solvent initial heating mdin
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=1000, ntwx=1000, nstlim=200000,
> dt=0.002, ntt=3, gamma_ln=5.0, ig=-1,
> ntc=2, ntf=2, cut=8, ntb=1,
> iwrap=1, ioutfm=1, nmropt=1,
> tempi = 150.0, temp0 = 200.0
> /
> &wt
> TYPE='TEMP0', ISTEP1=0, ISTEP2=150000,
> VALUE1=160.0, VALUE2=200.0,
> /
> &wt TYPE='END' /
>Heat 5
>Explicit solvent initial heating mdin
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=1000, ntwx=1000, nstlim=200000,
> dt=0.002, ntt=3, gamma_ln=5.0, ig=-1,
> ntc=2, ntf=2, cut=8, ntb=1,
> iwrap=1, ioutfm=1, nmropt=1,
> tempi = 200.0, temp0 = 250.0
> /
> &wt
> TYPE='TEMP0', ISTEP1=0, ISTEP2=150000,
> VALUE1=210.0, VALUE2=250.0,
> /
> &wt TYPE='END' /
>Heat 6
>Explicit solvent initial heating mdin
> &cntrl
> imin=0, irest=0, ntx=1,
> ntpr=1000, ntwx=1000, nstlim=200000,
> dt=0.002, ntt=3, gamma_ln=5.0, ig=-1,
> ntc=2, ntf=2, cut=8, ntb=1,
> iwrap=1, ioutfm=1, nmropt=1,
> tempi = 250.0, temp0 = 300.0
> /
> &wt
> TYPE='TEMP0', ISTEP1=0, ISTEP2=150000,
> VALUE1=260.0, VALUE2=300.0,
> /
> &wt TYPE='END' /
>
>By the end of sixth stage the temperature graph was plotted and it shows
>fluctuations (please find the attached copy of the plot) I wish to know
>whether the output is fine and the heating went through normally. I would
>like to point that when we run heating in a single stage from 0 to 300 K
>these fluctuations were not observed.
>Any suggestions are welcome.
>
>Regards
>
>
>
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Received on Tue Oct 13 2015 - 02:30:03 PDT
