AMBER Archive (2005)

Subject: Re: AMBER: temprature and restraint in constant volumm MD

From: tonglei (xbcdnana_at_gmail.com)
Date: Mon Nov 21 2005 - 07:56:12 CST

Thank you very much
  The Amber version I used is Amber 8.
    My input files is:
        molecular dynamics run
 &cntrl
     nmropt=1, vlimit=20,
    imin=0,irest=0,ntx=1,
    tempi=0.0,temp0=300,tautp=1.0,
    ntt=1,npscal=1,nsnb=25,
    ntp=0,ntb=1,ntr=1,
    ntc=2,ntf=2,scee=1.2,
    nstlim=25000,dt=0.002,
    ntwx=500,ntpr=25,ntwr=500,
    cut=12.0,
 &end
 &wt
   type='TEMP0',istep1=0,istep2=2500,
                value1=0.0,value2=50.0,
 &end
 &wt
   type='TEMP0',istep1=2500,istep2=5000,
                value1=50.0,value2=100.0,
 &end
 &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
 &wt
   type='TEMP0',istep1=10000,istep2=15000,
                value1=200.0,value2=300.0,
 &end
 &wt
   type='TEMP0',istep1=15000,istep2=25000,
                value1=300.0,value2=300.0,
 &end
 &wt
   type='END',
 &end
 &rst
   iat=0,
 &end
Restrain the Protein heavy atoms I
5.0
FIND
 * C * *
 * CA * *
 * CB * *
 * CC * *
 * CD * *
 * CE * *
 * CG * *
 * CZ * *
 * CH * *
SEARCH
RES 1 350
END
Restrain the Protein heavy atoms II
5.0
FIND
 * N * *
 * NH * *
 * ND * *
 * NE * *
 * NZ * *
 * O * *
 * OG * *
 * OH * *
 * OE * *
SEARCH
RES 1 350
END
Restrain the Protein heavy atoms III
5.0
FIND
 * P * *
 * SG * *
 * O1P * *
 * O2P * *
 * O3P * *
SEARCH
RES 1 350
END
Restrain the peptide heavy atoms I
5.0
FIND
 * C * *
 * CA * *
 * CB * *
 * CC * *
 * CD * *
 * CE * *
 * CG * *
 * CZ * *
 * CH * *
SEARCH
RES 351 368
END
Restrain the peptide heavy atoms II
5.0
FIND
 * N * *
 * NH * *
 * ND * *
 * NE * *
 * NZ * *
 * O * *
 * OE * *
SEARCH
RES 351 368
END
END

    After this procedure, I found the complex is almost identical with
my reference structure(leap.mdcrd, leap.pdb) without any changes, that
is to say, the complex wasn't affected any more in the course of
temprature raising. The 5kcal force was put on the heavy atoms exept H
atom.
  thank you 

--
 Na Zhang
 Chemistry Department
 Zhejiang University PRC
 xbcdnana_at_gmail.com
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu