Hi,
I have a big system wherein I have fixed some atoms. I am trying to run aMD
using NVT in AMBER16. I have considered protein as solute. The input script
is below
&cntrl
imin=0,irest=1,ntx=5,
nstlim=5000000,dt=0.002,
ntc=2,ntf=2,ig=-1,iwrap=1,
cut=12.0, ntb=1, ntp=0,
ntpr=5000,
ntwx=5000,ntwr=5000,
ntt=3,
gamma_ln=2.0,
temp0=310.0,
iamd=3,
ethreshd=1724.94, alphad=91.2,
ethreshp=-4750480.49, alphap=42260.64,
ntr=1,
restraintmask=":PAP,OAP,CAP",
restraint_wt=2.0,
/
The job is running with the following output below. The output file prints
boost potential. However, even after few steps the amd1.log file is empty.
I am using this command to run aMD.
mpirun -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -i amd.in -o amd1.out -p
solvated.prmtop -c nvt2.rst -r amd1.rst -x amd1.mdcrd -amd amd1.log -ref
nvt2.rst
Does aMD in amber outputs log file at a certain interval or does it output
simultaneously? Is something wrong with my input script?
Feedback is appreciated.
Many thanks,
Neha
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.7967E-11 at 2.716640
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.27
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.78
|---------------------------------------------------
NSTEP = 5000 TIME(PS) = 16010.000 TEMP(K) = 310.26 PRESS =
0.0
Etot = -4551453.8170 EKtot = 201600.6094 EPtot =
-4753054.4264
BOND = 14755.9824 ANGLE = 296072.4666 DIHED =
1665.8838
1-4 NB = 409.8328 1-4 EEL = 5227.4676 VDWAALS =
291153.8364
EELEC = -5367843.8248 EHBOND = 0.0000 RESTRAINT =
5313.7813
EAMBER (non-restraint) = -4758368.2077
EAMD_BOOST = 190.1475
------------------------------------------------------------------------------
NSTEP = 10000 TIME(PS) = 16020.000 TEMP(K) = 310.55 PRESS =
0.0
Etot = -4551155.4562 EKtot = 201785.0938 EPtot =
-4752940.5499
BOND = 14619.5673 ANGLE = 296188.9432 DIHED =
1668.0821
1-4 NB = 424.3435 1-4 EEL = 5205.6053 VDWAALS =
291448.0118
EELEC = -5368040.0905 EHBOND = 0.0000 RESTRAINT =
5371.0971
EAMBER (non-restraint) = -4758311.6470
EAMD_BOOST = 173.8903
------------------------------------------------------------------------------
NSTEP = 15000 TIME(PS) = 16030.000 TEMP(K) = 310.02 PRESS =
0.0
Etot = -4551659.6243 EKtot = 201441.3750 EPtot =
-4753100.9993
BOND = 14629.6002 ANGLE = 296205.6802 DIHED =
1675.9957
1-4 NB = 426.8043 1-4 EEL = 5301.2174 VDWAALS =
291497.5087
EELEC = -5368374.3098 EHBOND = 0.0000 RESTRAINT =
5346.1754
EAMBER (non-restraint) = -4758447.1747
EAMD_BOOST = 190.3287
------------------------------------------------------------------------------
NSTEP = 20000 TIME(PS) = 16040.000 TEMP(K) = 309.83 PRESS =
0.0
Etot = -4551891.5960 EKtot = 201317.7969 EPtot =
-4753209.3928
BOND = 14829.0396 ANGLE = 296273.2267 DIHED =
1663.7303
1-4 NB = 416.0436 1-4 EEL = 5265.0791 VDWAALS =
290884.6786
EELEC = -5368130.1728 EHBOND = 0.0000 RESTRAINT =
5376.0214
EAMBER (non-restraint) = -4758585.4143
EAMD_BOOST = 212.9606
------------------------------------------------------------------------------
NSTEP = 25000 TIME(PS) = 16050.000 TEMP(K) = 309.87 PRESS =
0.0
Etot = -4551477.6976 EKtot = 201346.5469 EPtot =
-4752824.2445
BOND = 14599.0113 ANGLE = 296236.5187 DIHED =
1668.0522
1-4 NB = 407.2572 1-4 EEL = 5270.1186 VDWAALS =
290649.7462
EELEC = -5367173.8419 EHBOND = 0.0000 RESTRAINT =
5359.4243
EAMBER (non-restraint) = -4758183.6687
EAMD_BOOST = 159.4690
------------------------------------------------------------------------------
NSTEP = 30000 TIME(PS) = 16060.000 TEMP(K) = 310.49 PRESS =
0.0
Etot = -4551482.3537 EKtot = 201745.9375 EPtot =
-4753228.2912
BOND = 14617.9310 ANGLE = 295988.0059 DIHED =
1682.9548
1-4 NB = 417.0034 1-4 EEL = 5284.7779 VDWAALS =
291148.8386
EELEC = -5367850.0502 EHBOND = 0.0000 RESTRAINT =
5277.9244
EAMBER (non-restraint) = -4758506.2156
EAMD_BOOST = 204.3229
------------------------------------------------------------------------------
NSTEP = 35000 TIME(PS) = 16070.000 TEMP(K) = 309.38 PRESS =
0.0
Etot = -4552032.8399 EKtot = 201028.9688 EPtot =
-4753061.8087
BOND = 14744.4027 ANGLE = 296278.0674 DIHED =
1668.3239
1-4 NB = 412.3627 1-4 EEL = 5243.8350 VDWAALS =
290585.8380
EELEC = -5367522.5373 EHBOND = 0.0000 RESTRAINT =
5338.2874
EAMBER (non-restraint) = -4758400.0961
EAMD_BOOST = 189.6114
------------------------------------------------------------------------------
NSTEP = 40000 TIME(PS) = 16080.000 TEMP(K) = 310.24 PRESS =
0.0
Etot = -4551536.1379 EKtot = 201586.8281 EPtot =
-4753122.9661
BOND = 14562.8873 ANGLE = 295915.7131 DIHED =
1665.8909
1-4 NB = 407.2010 1-4 EEL = 5221.5786 VDWAALS =
291309.0573
EELEC = -5367752.7319 EHBOND = 0.0000 RESTRAINT =
5347.9815
EAMBER (non-restraint) = -4758470.9475
EAMD_BOOST = 199.4562
------------------------------------------------------------------------------
NSTEP = 45000 TIME(PS) = 16090.000 TEMP(K) = 310.18 PRESS =
0.0
Etot = -4551506.1157 EKtot = 201548.4219 EPtot =
-4753054.5375
BOND = 14782.9000 ANGLE = 295969.5275 DIHED =
1686.8929
1-4 NB = 413.5688 1-4 EEL = 5241.3845 VDWAALS =
292092.9809
EELEC = -5368732.1772 EHBOND = 0.0000 RESTRAINT =
5312.2337
EAMBER (non-restraint) = -4758366.7712
EAMD_BOOST = 178.1512
------------------------------------------------------------------------------
NSTEP = 50000 TIME(PS) = 16100.000 TEMP(K) = 310.04 PRESS =
0.0
Etot = -4551315.2092 EKtot = 201459.3906 EPtot =
-4752774.5998
BOND = 14773.5232 ANGLE = 295854.9629 DIHED =
1650.8962
1-4 NB = 406.1880 1-4 EEL = 5289.8532 VDWAALS =
291646.2125
EELEC = -5368016.5140 EHBOND = 0.0000 RESTRAINT =
5455.4163
EAMBER (non-restraint) = -4758230.0162
EAMD_BOOST = 164.8618
------------------------------------------------------------------------------
NSTEP = 55000 TIME(PS) = 16110.000 TEMP(K) = 309.69 PRESS =
0.0
Etot = -4551490.5131 EKtot = 201226.0312 EPtot =
-4752716.5444
BOND = 14876.5579 ANGLE = 296080.8470 DIHED =
1677.1978
1-4 NB = 409.3799 1-4 EEL = 5249.4844 VDWAALS =
290139.9473
EELEC = -5366676.5489 EHBOND = 0.0000 RESTRAINT =
5385.2637
EAMBER (non-restraint) = -4758101.8081
EAMD_BOOST = 141.3265
------------------------------------------------------------------------------
NSTEP = 60000 TIME(PS) = 16120.000 TEMP(K) = 308.46 PRESS =
0.0
Etot = -4552691.6421 EKtot = 200430.7812 EPtot =
-4753122.4233
BOND = 14819.7514 ANGLE = 295979.2229 DIHED =
1684.8899
1-4 NB = 420.1780 1-4 EEL = 5265.5505 VDWAALS =
290659.7122
EELEC = -5367558.3499 EHBOND = 0.0000 RESTRAINT =
5418.2259
EAMBER (non-restraint) = -4758540.6493
EAMD_BOOST = 188.3957
------------------------------------------------------------------------------
NSTEP = 65000 TIME(PS) = 16130.000 TEMP(K) = 309.85 PRESS =
0.0
Etot = -4551736.6218 EKtot = 201334.5156 EPtot =
-4753071.1374
BOND = 14794.1830 ANGLE = 296091.6206 DIHED =
1655.4728
1-4 NB = 398.9510 1-4 EEL = 5283.5602 VDWAALS =
290863.8268
EELEC = -5367786.0015 EHBOND = 0.0000 RESTRAINT =
5428.0322
EAMBER (non-restraint) = -4758499.1696
EAMD_BOOST = 199.2174
------------------------------------------------------------------------------
NSTEP = 70000 TIME(PS) = 16140.000 TEMP(K) = 310.07 PRESS =
0.0
Etot = -4551544.0362 EKtot = 201472.9219 EPtot =
-4753016.9580
BOND = 14592.0523 ANGLE = 296161.7418 DIHED =
1689.9267
1-4 NB = 413.4779 1-4 EEL = 5286.3279 VDWAALS =
290726.9576
EELEC = -5367482.9266 EHBOND = 0.0000 RESTRAINT =
5423.8127
EAMBER (non-restraint) = -4758440.7707
EAMD_BOOST = 171.6717
------------------------------------------------------------------------------
NSTEP = 75000 TIME(PS) = 16150.000 TEMP(K) = 309.72 PRESS =
0.0
Etot = -4551660.6392 EKtot = 201247.5781 EPtot =
-4752908.2174
BOND = 14711.3855 ANGLE = 296215.6832 DIHED =
1682.9370
1-4 NB = 400.9849 1-4 EEL = 5278.7700 VDWAALS =
290672.6372
EELEC = -5367454.6360 EHBOND = 0.0000 RESTRAINT =
5422.8114
EAMBER (non-restraint) = -4758331.0288
EAMD_BOOST = 161.2094
------------------------------------------------------------------------------
NSTEP = 80000 TIME(PS) = 16160.000 TEMP(K) = 309.97 PRESS =
0.0
Etot = -4551621.5616 EKtot = 201412.4219 EPtot =
-4753033.9835
BOND = 14823.7155 ANGLE = 296283.1154 DIHED =
1653.1091
1-4 NB = 414.8876 1-4 EEL = 5261.5953 VDWAALS =
290595.3249
EELEC = -5367689.1917 EHBOND = 0.0000 RESTRAINT =
5427.6015
EAMBER (non-restraint) = -4758461.5850
EAMD_BOOST = 195.8589
------------------------------------------------------------------------------
NSTEP = 85000 TIME(PS) = 16170.000 TEMP(K) = 309.45 PRESS =
0.0
Etot = -4551858.9002 EKtot = 201073.3594 EPtot =
-4752932.2596
BOND = 14799.3615 ANGLE = 296211.3577 DIHED =
1646.6029
1-4 NB = 430.9926 1-4 EEL = 5324.5321 VDWAALS =
290217.5794
EELEC = -5367093.4287 EHBOND = 0.0000 RESTRAINT =
5343.5453
EAMBER (non-restraint) = -4758275.8049
EAMD_BOOST = 187.1977
------------------------------------------------------------------------------
NSTEP = 90000 TIME(PS) = 16180.000 TEMP(K) = 309.71 PRESS =
0.0
Etot = -4552007.6431 EKtot = 201239.4219 EPtot =
-4753247.0650
BOND = 14511.5040 ANGLE = 295982.0713 DIHED =
1674.9199
1-4 NB = 409.7197 1-4 EEL = 5223.8292 VDWAALS =
290457.4761
EELEC = -5367163.4649 EHBOND = 0.0000 RESTRAINT =
5445.3630
EAMBER (non-restraint) = -4758692.4280
EAMD_BOOST = 211.5168
------------------------------------------------------------------------------
NSTEP = 95000 TIME(PS) = 16190.000 TEMP(K) = 310.97 PRESS =
0.0
Etot = -4550948.8701 EKtot = 202059.9062 EPtot =
-4753008.7764
BOND = 14813.8430 ANGLE = 296205.3117 DIHED =
1675.9792
1-4 NB = 417.9633 1-4 EEL = 5247.5664 VDWAALS =
291174.0612
EELEC = -5368180.8324 EHBOND = 0.0000 RESTRAINT =
5459.3460
EAMBER (non-restraint) = -4758468.1224
EAMD_BOOST = 177.9852
------------------------------------------------------------------------------
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
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Received on Wed Nov 09 2016 - 03:00:03 PST
