I can't open your attached file. It's easier if you attach inputs as
text files.
It looks like you have defined your heating starting at step 5000, but
have not
defined a vlue for steps 0-5000. In that case it will use TEMP0 from the
namelist part of the input. What is that value? You probably should define
the temp0 weight change for all steps of the simulation.
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
Shulin Zhuang wrote:
>Dear,
>
>I have met with a strange problem.
>
>When I perform the constant volume MD of a protein-ligand complex to
>raise the temperatur from 0k to 300K, the temperature raise so quikly
>that after 12 ps, it reach 300K. I have examined the one snapshot from
>the constant volume MD and find the ligand conformation is much
>differenct from the crystal and two hydrogen bonds lost.
>
>Therefore I have to do the restraint MD to control the temperature.
>
>The prmtop file and inpcrd file are made with amber8 using ff03.
>
>When I use amber8 to perform the restraint MD, it fails and give the
>following error:
>
>GROUP 1 HAS HARMONIC CONSTRAINTS -4.00000
> rfree: Error decoding variable 2 2 from:
>Restrain the
> this indicates that your input contains
> incorrect information
>
>But I use the same input file to perform restraint MD with amber7, it
>is successful and no error occurs.
>
>But I examine the amber7 output and find that, the temperature are not
>under control.
>
>What is the problem? How should I tackle it?
>
>I set the temperature control that:
>&wt
> type='TEMP0',istep1=5000,istep2=7500,
> value1=100.0,value2=150.0,
> &end
>
>&wt
> type='TEMP0',istep1=7500,istep2=10000,
> value1=150.0,value2=200.0,
> &end
>
>The time step is 0.002 ps.
>
>According to the temperature control, the temperature should under 150
>K before 15 ps(etc. 7500 steps), however, after 10.4 ps, the
>temperature exceed 150 K.
>At 15 ps, the temp is 296.7 K, after this the temp decrease, and at
>20 ps the temp is 194.39 K. After 20 ps, the temp raise slowly.
>
>Does the tempearature change normally?
>
>
>The partial output file and input file are attached.
>
>Thanks a lot!
>
>Best regards
>shulin
>
>
>
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Received on Fri May 13 2005 - 12:53:00 PDT
