AMBER Archive (2006)

Subject: Re: RE: Re: AMBER: A question about Dynamics.

From: Qingning Shu (qshu_at_mail.rx.uga.edu)
Date: Fri Sep 22 2006 - 17:28:54 CDT

Dear Sir:
Thank you for your reply. I really carefully check the output files. But I didn't see anything suspicious. At the beginning of second simulation, even the temperature dropped. The following is the files and sander commands I used.
SHU

vac_md0.in
  &cntrl
  IREST=0, NTR=1,
  igb=1, NTPR=200, NTWX=200,
  ntt=3, gamma_ln=1.0,
  NTX=1, TEMPI=0.0,
  NTB=0,
  TEMP0=300.0,
  NTP=0,
  NSTLIM=100000, DT=0.0005,
  NTC=2, NTF=2,
  CUT=999.0, rgbmax=999,
 &end
Restraint
5.00
RES 1 58
RES 62 293
RES 295 312
RES 333 354
RES 359 375
RES 380 401
RES 407 431
RES 434 506
END
END

sander -O -i vac_md0.in -p vac.prmtop -c vac_min.rst -x vac_md0.crd -r vac_md0.rst -o vac_md0.out -ref vac_min.rst

vac_md0.out
 NSTEP = 100000 TIME(PS) = 50.000 TEMP(K) = 299.33 PRESS = 0.0
 Etot = -5971.8009 EKtot = 5840.6603 EPtot = -11812.4612
 BOND = 1447.8574 ANGLE = 3853.9765 DIHED = 4589.1826
 1-4 NB = 1797.9992 1-4 EEL = 21668.6620 VDWAALS = -3847.5250
 EELEC = -35196.3878 EGB = -7311.3802 RESTRAINT = 1185.1540
 EAMBER (non-restraint) = -12997.6152

vac_md1.in
 &cntrl
  IREST=1, NTX=7,
  NTR=1,
  igb=1, NTPR=20, NTWX=20,
  ntt=3, gamma_ln=1.0,
  TEMPI=300.0,
  NTB=0,
  TEMP0=300.0,
  NTP=0,
  NSTLIM=10000, DT=0.001,
  NTC=2, NTF=2,
  CUT=999.0, rgbmax=999,
 &end
Restraint
5.00
RES 1 58
RES 62 293
RES 295 312
RES 333 354
RES 359 375
RES 380 401
RES 407 431
RES 434 506
END
END

sander -O -i vac_md1.in -p vac.prmtop -c vac_md0.rst -x vac_md1.crd -r vac_md1.rst -o vac_md1.out -ref vac_md0.rst

vac_md1.out
 NSTEP = 20 TIME(PS) = 50.020 TEMP(K) = 261.54 PRESS = 0.0
 Etot = -7141.0608 EKtot = 5103.1593 EPtot = -12244.2201
 BOND = 1397.4627 ANGLE = 3842.0300 DIHED = 4507.9623
 1-4 NB = 1806.0591 1-4 EEL = 21696.4855 VDWAALS = -3809.2416
 EELEC = -35236.0756 EGB = -7293.9714 RESTRAINT = 845.0689
 EAMBER (non-restraint) = -13089.2890
 ------------------------------------------------------------------------------

-----Original Message-----
From: "Ross Walker" <ross_at_rosswalker.co.uk>
To: <amber_at_scripps.edu>
Date: Thu, 21 Sep 2006 08:58:08 -0700
Subject: RE: Re: AMBER: A question about Dynamics.

Dear Shu,

> Thank you for your reply. But I checked the .in files again.
> There is no problem. And I found that even the
> temperatureVs.time plot had a drop. Following is the two .in
> files. Thank you.
>
> SHU
>
> md0.in
> &cntrl
> IREST=0, NTX=1,
> igb=1, NTPR=200, NTWX=200,
> ntt=3, gamma_ln=1.0,
> NTR=1, TEMPI=0.0,
> NTB=0,
> TEMP0=300.0,
> NTP=0,
...

This is not enough information for us to help you. What command line options
did you use, what size was the energy drop? If you compare the final output
from the first trajectory and the first output from the new trajectory where
are the differences?

Have you changed the structure you are restraining to? E.g. did simulation 1
restrain to the initial inpcrd file and then simulation 2 restrain to the
restart file from simulation 1? In this case the discontinuity in the
potential energy will be due to the restraint energy changing.

As Dave suggests take a 'careful' look at the output from your two
simulations. Set up the new run to do only 1 step so that you get the
energies for the first structure in this simulation. Then compare every
energy term with the final results from the previous simulation. This will
tell you where to start looking to explain what is going on.

All the best
Ross

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|\oss Walker

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| San Diego Supercomputer Center |
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