On Tue, Feb 20, 2007, Ruchi Sachdeva wrote:
> Hi,
>
> My problen has not been solved yet. Kindly acknowledge if you have
> received this email and please forward it to the list.
>
>
> Dear AMBER users
>
> Im trying to run REMD with torsional restraints on alpha helix residues
> using AMBER8 (ff99) on Linux cluster. Although exchanges were being allowed
> between replicas but target temperatures were not getting swapped between
> the replicas, as indicated in the rem.log file. Same torsional restraints
> were applied to all the replicas.
>
> But when torsional restraints were not applied, REMD was running fine
> & target tempeatures got exchanged.
>
> I did this as follows:
>
> Step1 - First I did initial minimization of 25000 steps in implicit
> solvent, igb=1, without any torsional restraints.
>
> Step2 - The system was heated to 300K for 100 ps using berendsen
> thermostat. Torsional restraints were also applied.
>
> Step3 - Equilibration was carried out at 300K for 1000ps. Again
> torsional restraints were applied.
>
> Step4 - 4 copies of the resulting coordinates ( i.e. md2.rst) were
> made. Each replica was independently equilibrated at its own temperature
> i.e. 275, 282, 289, 296K for 1000ps, alongwith torsional restraints.
>
> I am showing the input file for replica-0 only. Input files for other
> replicas differed only in target temperature.
>
> equil0.in
> Equilibration of replica-0 at 275K for 1000 ps, igb = 1, with torsional
> restraints on residues forming alpha helix & beta sheet
> &cntrl
> imin = 0, ntb = 0,
> irest = 1, ntx = 5,
> igb = 1, ntpr = 1000, ntwx = 1000, ntwr = 1000,
> ntt = 1, tautp = 1.0,
> tempi = 275.0, temp0 = 275.0,
> ntc = 2, ntf = 2,
> nstlim = 500000, dt = 0.002,
> cut = 999, vlimit = 25, nmropt = 1
> /
>
> &wt type='REST', istep1=0, istep2=10000, value1=0.1,
> value2=1.0, /
> &wt type='REST', istep1=10001, istep2=500000, value1=1.0,
> value2=1.0, /
>
> &wt type='END' /
> LISTIN=POUT
> DISANG=RST.ci
>
>
>
> Step 5 - The final configurations (i.e. equil.rst.000, equil.rst.001,
> equil.rst.002, equil.rst.003) of these equilibrations were taken as input
> coordinates for REMD. Same restraints i.e. same RST file was used for each
> replica.
>
> 4 input files were made. Only the target temperature was different in
> these files, rest of the variables were same. I am showing just 2 files :
>
> rem.in.000
> REMD run with torsional restraints on alpha helix residues, igb=1, AMBER8
> &cntrl
> imin = 0, nstlim = 2500, dt = 0.002,
> ntx = 5, tempi = 0.0, temp0 = 275.0,
> ntt = 1, tol = 0.000001, saltcon = 0.2,
> ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
> ntwx = 100, ntwe = 0, ntwr = 200, ntpr = 100,
> scee = 1.2, cut = 99.0,
> ntr = 0, tautp = 0.1, offset = 0.09,
> nscm = 500, igb = 1, numexchg = 10,
> irest = 1, ntave = 0, vlimit = 25, nmropt = 1
> /
>
>
> &wt type='REST', istep1=0, istep2=100, value1=0.1,
> value2=1.0, /
> &wt type='REST', istep1=101, istep2=2500, value1=1.0,
> value2=1.0, /
>
> &wt type='END' /
> LISTIN=POUT
> DISANG=RST
>
>
> rem.in.001
> REMD run with torsional restraints on alpha helix residues, igb=1, AMBER8
> &cntrl
> imin = 0, nstlim = 2500, dt = 0.002,
> ntx = 5, tempi = 0.0, temp0 = 282.0,
> ntt = 1, tol = 0.000001, saltcon = 0.2,
> ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
> ntwx = 100, ntwe = 0, ntwr = 200, ntpr = 100,
> scee = 1.2, cut = 99.0,
> ntr = 0, tautp = 0.1, offset = 0.09,
> nscm = 500, igb = 1, numexchg = 10,
> irest = 1, ntave = 0, vlimit = 25, nmropt = 1
> /
>
>
> &wt type='REST', istep1=0, istep2=100, value1=0.1,
> value2=1.0, /
> &wt type='REST', istep1=101, istep2=2500, value1=1.0,
> value2=1.0, /
>
> &wt type='END' /
> LISTIN=POUT
> DISANG=RST
>
>
> I got following rem.log file:
>
> # replica exchange log file
> # Replica #, Velocity Scaling Factor, T, Eptot, Temp0, NewTemp0
> # exchange 1
> 1 -1.00 279.93 -2015.51 275.00 275.00
> 2 -1.00 278.93 -1951.14 282.00 282.00
> 3 -1.00 288.59 -1960.63 289.00 289.00
> 4 -1.00 285.23 -1913.25 296.00 296.00
> # exchange 2
> 1 -1.00 272.73 -1993.13 275.00 275.00
> 2 1.01 272.77 -1924.55 ** 282.00 ** 289.00
> 3 0.99 289.04 -1951.70 ** 289.00 ** 282.00
> 4 -1.00 299.82 -1950.95 296.00 296.00
> # exchange 3
> 1 -1.00 270.77 -2011.05 275.00 275.00
> 2 -1.00 284.21 -1970.67 ** 282.00 ** 282.00
> 3 -1.00 292.72 -1977.76 ** 289.00 ** 289.00
> 4 -1.00 301.78 -1946.56 296.00 296.00
> # exchange 4
> 1 -1.00 278.82 -2038.74 275.00 275.00
> 2 -1.00 286.11 -1989.72 282.00 282.00
> 3 -1.00 290.02 -1955.69 289.00 289.00
> 4 -1.00 302.56 -1949.02 296.00 296.00
> # exchange 5
> 1 -1.00 277.76 -2038.56 275.00 275.00
> 2 -1.00 283.52 -1967.68 282.00 282.00
> 3 -1.00 293.98 -1965.70 289.00 289.00
> 4 -1.00 288.43 -1914.41 296.00 296.00
> # exchange 6
> 1 -1.00 274.67 -2043.14 275.00 275.00
> 2 1.01 281.29 -1974.33 282.00 289.00
> 3 0.99 294.38 -1971.34 289.00 282.00
> 4 -1.00 295.38 -1937.41 296.00 296.00
> # exchange 7
> 1 -1.00 272.07 -2015.42 275.00 275.00
> 2 -1.00 283.13 -1963.17 282.00 282.00
> 3 -1.00 299.59 -1991.40 289.00 289.00
> 4 -1.00 291.96 -1923.93 296.00 296.00
> # exchange 8
> 1 -1.00 269.27 -2014.54 275.00 275.00
> 2 1.01 289.24 -1980.72 282.00 289.00
> 3 0.99 284.76 -1954.30 289.00 282.00
> 4 -1.00 295.82 -1930.07 296.00 296.00
> # exchange 9
> 1 -1.00 273.25 -2028.57 275.00 275.00
> 2 -1.00 282.23 -1977.14 282.00 282.00
> 3 1.01 278.57 -1912.78 289.00 296.00
> 4 0.99 304.64 -1956.62 296.00 289.00
> # exchange 10
> 1 -1.00 277.65 -2040.60 275.00 275.00
> 2 1.01 285.22 -1982.82 282.00 289.00
> 3 0.99 291.23 -1976.79 289.00 282.00
> 4 -1.00 292.41 -1918.82 296.00 296.00
>
>
> As we can see from the rem.log file that during exchange attempt 2,
> exchange is allowed between replica pair 2 & 3 (marked as star). But after
> exchange attempt 3, the current target temperature of replica 2 is still
> 282K and of replica 3 is still 289K (marked as star). Rather they must be
> 289 & 282K respectively as the exchange has been allowed prior to Sander
> call. We can notice such kind of behaviour in further exchange attempts
> and with other replicas.
>
> This indicates that the target tempratures are not being swapped even when
> the exchange is allowed.
>
> ******* However when I didnt apply torsional restraints, REMD was running
> fine. Temperatures swapping did occur. *********
>
> Have I followed the right protocol? Please check out the files and tell me
> where Im wrong and give some suggestions.
>
> Thanks in advance!!!!
>
> Ruchi
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | skype: dacase
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Wed Feb 28 2007 - 06:07:28 PST
