Dear AMBER people,
I am doing equilibration of my system (a protein in a periodic box with
water)
and using the option VRAND to set random velocities to water molecules
(protein
atoms are frozen with belly) at T=300K every 50 steps. I am not using
any other
temperature coupling schemes with VRAND flag turned on (NTT=0).
But the velocities seem assigned at 260K instead of 300K:
Setting new random velocities at step 50
NSTEP = 50 TIME(PS) = 0.100 TEMP(K) = 390.42 PRESS =
-685.24
Etot = -61709.3702 EKtot = 18699.2761 EPtot =
-80408.6463
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
10068.3742
EELEC = -90477.0206 EHBOND = 0.0000 CONSTRAINT =
0.0000
EKCMT = 7813.8636 VIRIAL = 12567.0927 VOLUME =
321268.1614
Density =
0.8118
Ewald error estimate: 0.1023E-03
------------------------------------------------------------------------------
NSTEP = 51 TIME(PS) = 0.102 TEMP(K) = 260.63 PRESS =
-892.05
Etot = -67918.0705 EKtot = 12482.8609 EPtot =
-80400.9314
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
10086.0421
EELEC = -90486.9735 EHBOND = 0.0000 CONSTRAINT =
0.0000
EKCMT = 6268.8999 VIRIAL = 12455.9241 VOLUME =
321228.8301
Density =
0.8119
Ewald error estimate: 0.1363E-03
------------------------------------------------------------------------------
NSTEP = 52 TIME(PS) = 0.104 TEMP(K) = 260.62 PRESS =
-880.21
Etot = -67918.4786 EKtot = 12482.2785 EPtot =
-80400.7571
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
10102.5523
EELEC = -90503.3094 EHBOND = 0.0000 CONSTRAINT =
0.0000
EKCMT = 6270.9000 VIRIAL = 12374.8228 VOLUME =
321177.6518
Density =
0.8120
Ewald error estimate: 0.1331E-03
Since it's very likely that this feature is related to the wrong number
of degrees of freedom, I tried to run the same dynamics, but with all
atoms allowed to move
and without SHAKE (IBELLY=0, NTC=1). I also tried to use different
NDFMIN and NTCM/NSCM values.
But the result always turned out to be the same.
So my question is why the velocities are assigned at 260K instead of
300K?
Thanks in advance
Sveta
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Svetlana B. Nolde Email: sveta_at_nmr.ru
Shemyakin and Ovchinnikov Institute of
Bioorganic Chemistry Phone: +7-095-330-7483
Ul. Miklukho-Maklaya 16/10 Fax: +7-095-335-5033
Moscow 117997 Russia URL: http://www.nmr.ru/
-------------------------------------------------------------------------------
Received on Mon Apr 02 2001 - 09:17:01 PDT
