---------- Forwarded message ----------
From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Thu, May 31, 2012 at 4:58 PM
Subject: Fwd: problem with running equilibration MD in an LES system
To: AMBER Mailing List <amber.ambermd.org>
A small addition to the previous email. In mdin.3 I tried with tempi=300.0.
Still the result is the same.
---------- Forwarded message ----------
From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Thu, May 31, 2012 at 4:39 PM
Subject: problem with running equilibration MD in an LES system
To: AMBER Mailing List <amber.ambermd.org>
Hi all,
After heating my system up to 300K with the mdin.2 input file (shown below)
I am trying to equilibrate my system at 300K (gradually removing
constraints) using mdin.3 input file (shown below). Instead of starting at
300K and proceeding at 300K the simulation starts at a temperature of 200K
and increases temperature at every step. I really cannot figure out why
that happens. I would really appreciate if you can suggest a solution.
Given below are my input scripts and the corresponding output.
mdin.2 (heating up in 6 picoseconds)
LPO
&cntrl
ntx=1, irest=0,
nsnb=1,
ntpr=100, ntwx=1000, ntwv=00,
nstlim=6000, t=0.00, dt=0.00100,
ntc = 2, ntf = 2,
ntb = 0,
ntt=1, temp0=010.0, tempi=010.0, tautp=0.001, vlimit=20.0,
ntr = 1,
cut = 12.0,
dielc=1,
nmropt=1
/
&ewald
eedmeth = 5,
&end
&wt type='TEMP0', istep1=00000, istep2=0500, value1=000., value2=010.,
&end
&wt type='TEMP0', istep1=0501, istep2=1000, value1=010., value2=020., &end
&wt type='TEMP0', istep1=1001, istep2=1500, value1=020., value2=050., &end
&wt type='TEMP0', istep1=1501, istep2=2000, value1=050., value2=100., &end
&wt type='TEMP0', istep1=2001, istep2=3000, value1=100., value2=150., &end
&wt type='TEMP0', istep1=3001, istep2=4000, value1=150., value2=200., &end
&wt type='TEMP0', istep1=4001, istep2=5000, value1=200., value2=250., &end
&wt type='TEMP0', istep1=5001, istep2=6000, value1=250., value2=300., &end
&wt type='END' &end
HOLD PROTEIN FIXED
50.0
RES 1 996
END
END
mdin.3 (starting to remove constraints)
LPO
&cntrl
ntx=7, irest=1,
nsnb=1,
ntpr=100, ntwx=1000, ntwv=00,
nstlim=5000, t=0.00, dt=0.00100,
ntc = 2, ntf = 2,
ntb = 0,
ntt=1, temp0=300.0, tautp=1.0, vlimit=20.0,
ntr = 1,
cut = 12.0,
dielc = 1
&end
&ewald
eedmeth = 5,
&end
Hold protein fixed
40.0
RES 1 996
END
END
OUTPUT LOOKS LIKE
NSTEP = 100 TIME(PS) = 6.100 TEMP(K) = 204.60 PRESS =
0.0
Etot = 10340.7641 EKtot = 8001.9585 EPtot =
2338.8056
BOND = 1763.4131 ANGLE = 4615.7513 DIHED =
9894.0893
1-4 NB = 3335.5171 1-4 EEL = 13956.3961 VDWAALS =
-7776.3421
EELEC = -28105.2028 EHBOND = 0.0000 RESTRAINT =
4655.1836
EAMBER (non-restraint) = -2316.3780
------------------------------------------------------------------------------
NSTEP = 200 TIME(PS) = 6.200 TEMP(K) = 214.11 PRESS =
0.0
Etot = 10679.8642 EKtot = 8373.7012 EPtot =
2306.1630
BOND = 1820.6558 ANGLE = 4406.9515 DIHED =
9893.2709
1-4 NB = 3304.0287 1-4 EEL = 13989.3581 VDWAALS =
-7759.5507
EELEC = -28197.2735 EHBOND = 0.0000 RESTRAINT =
4848.7221
EAMBER (non-restraint) = -2542.5591
------------------------------------------------------------------------------
NSTEP = 300 TIME(PS) = 6.300 TEMP(K) = 222.86 PRESS =
0.0
Etot = 11046.9840 EKtot = 8716.0885 EPtot =
2330.8955
BOND = 1827.5852 ANGLE = 4430.9047 DIHED =
9863.7035
1-4 NB = 3340.9509 1-4 EEL = 14001.2412 VDWAALS =
-7730.2507
EELEC = -28230.1533 EHBOND = 0.0000 RESTRAINT =
4826.9141
EAMBER (non-restraint) = -2496.0186
------------------------------------------------------------------------------
NSTEP = 400 TIME(PS) = 6.400 TEMP(K) = 216.72 PRESS =
0.0
Etot = 11338.8244 EKtot = 8476.0088 EPtot =
2862.8157
BOND = 1882.1913 ANGLE = 4539.4416 DIHED =
9888.4405
1-4 NB = 3343.3038 1-4 EEL = 13997.3130 VDWAALS =
-7764.5399
EELEC = -28168.4315 EHBOND = 0.0000 RESTRAINT =
5145.0969
EAMBER (non-restraint) = -2282.2813
Thank you
Sajeewa Dewage
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Received on Fri Jun 01 2012 - 06:00:05 PDT
