Hi Amber Users,
I am doing a Normal MD simulation for a system with around 20000 atoms in
explicit solvent.
I am doing energy minimization with and without restrain, then I am doing
20ps equilibration with restarin and then 100ps equilibration with out
restrain. From then on I am running production run in 5ns segments.
I used pmemd.MPI module for all steps.
My input file for production run is as follows:
Production RUN for WILD TYPE SYSTEMIN
&cntrl
imin=0,
irest=1,
ntx=7,
*ntb=2, pres0=1.0, ntp=1, taup=2.0,*
cut=10.0,
ntc=2,
ntf=2,
tempi=298.0,
temp0=298.0,
ig=-1,
ntt=3,
gamma_ln=1.0,
nstlim=2500000,
dt=0.002,
ntpr=2000,
ntwx=2000,
ntwr=2000
/
When I analysed the mdout files I noticed that TEMP(K) is around 298K but
PRESS is not remaining constant. But density of the system is constant.
*---------------1st Production RUN--------- *
A V E R A G E S O V E R 1250 S T E P S
NSTEP = 2500000 TIME(PS) = 5120.000 TEMP(K) = 297.98 *PRESS
= 2.1*
Etot = -50822.7140 EKtot = 11702.0949 EPtot =
-62524.8089
BOND = 55.4592 ANGLE = 155.5385 DIHED =
228.1577
1-4 NB = 57.0438 1-4 EEL = 783.3743 VDWAALS =
9138.5839
EELEC = -72942.9663 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 5766.0990 VIRIAL = 5757.2274 VOLUME =
198807.0797
Density =
0.9906
Ewald error estimate: 0.8541E-04
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 2500000 TIME(PS) = 5120.000 TEMP(K) = 2.15 *PRESS =
136.5*
Etot = 150.1210 EKtot = 84.3845 EPtot =
118.3489
BOND = 6.0806 ANGLE = 10.0209 DIHED =
6.1697
1-4 NB = 3.4064 1-4 EEL = 13.0494 VDWAALS =
115.2660
EELEC = 184.0296 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 59.3527 VIRIAL = 584.4469 VOLUME =
295.4974
Density =
0.0015
Ewald error estimate: 0.6517E-04
*----------------2nd Production RUN------------*
A V E R A G E S O V E R 1250 S T E P S
NSTEP = 2500000 TIME(PS) = 10120.000 TEMP(K) = 298.00 *PRESS
= 3.4*
Etot = -50814.8089 EKtot = 11702.6850 EPtot =
-62517.4939
BOND = 55.2614 ANGLE = 154.7789 DIHED =
227.2959
1-4 NB = 56.9189 1-4 EEL = 784.4305 VDWAALS =
9139.6510
EELEC = -72935.8305 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 5762.9922 VIRIAL = 5748.5846 VOLUME =
198840.8726
Density =
0.9904
Ewald error estimate: 0.8746E-04
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 2500000 TIME(PS) = 10120.000 TEMP(K) = 2.09 *PRESS =
140.9*
Etot = 143.3059 EKtot = 81.9911 EPtot =
116.1555
BOND = 6.3690 ANGLE = 9.7132 DIHED =
6.2983
1-4 NB = 3.3909 1-4 EEL = 13.9009 VDWAALS =
115.3024
EELEC = 185.5990 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 56.6457 VIRIAL = 602.6782 VOLUME =
275.9059
Density =
0.0014
Ewald error estimate: 0.6569E-04
So my question "As I am running NPT simulation, should I be worried that
PRESS is not remaining constant or is the fluctuation is natural in AMBER?"
N.B: I have recently started MD simulation.
with regards
--
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
Mob:
8017650842
9681144106
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Received on Mon Jun 02 2014 - 04:00:02 PDT
