Hello, Scott!
I found out what kind of troubles occurs with
"gpu->sim.randomSteps = MAX_RANDOM_STEPS / 4;" instead of "=
MAX_RANDOM_STEPS;". Langevin thermostat start working wrong and gives weird
results. Temperature goes to 10-15 Kelvins above the target value; if
barostat is on, then system density goes down and, finally, after long run
simulated, protein becomes denatured. Changes are visible in the very
beginning of the simulation. It for sure can be avoided by increasing
coupling with thermostat and decreasing with barostat (I used gamma_ln=2,
taup=2), but the behavior of pmemd changed significantly, because that
combination worked well previously.
Example's here:
NSTEP = 1000 TIME(PS) = 15102.000 TEMP(K) = 307.53 PRESS =
197.3
Etot = -170456.3569 EKtot = 45170.3945 EPtot =
-215626.7514
BOND = 1191.7604 ANGLE = 3161.4808 DIHED =
4325.9739
1-4 NB = 1453.1637 1-4 EEL = 18231.0039 VDWAALS =
26643.2385
EELEC = -270633.3726 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 20851.1601 VIRIAL = 17748.7041 VOLUME =
728425.6016
Density =
1.0070
------------------------------------------------------------------------------
wrapping first mol.: 32.803756165308101 46.391515462057733
80.352455336984775
NSTEP = 2000 TIME(PS) = 15104.000 TEMP(K) = 306.54 PRESS =
364.6
Etot = -170356.7791 EKtot = 45024.9609 EPtot =
-215381.7400
BOND = 1200.8864 ANGLE = 3151.1249 DIHED =
4352.1928
1-4 NB = 1420.8669 1-4 EEL = 18185.7533 VDWAALS =
27177.9832
EELEC = -270870.5475 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 20618.3293 VIRIAL = 14843.0966 VOLUME =
733677.7903
Density =
0.9998
------------------------------------------------------------------------------
wrapping first mol.: 32.872779258382558 46.489128853446864
80.521526676727731
NSTEP = 3000 TIME(PS) = 15106.000 TEMP(K) = 308.29 PRESS =
116.8
Etot = -169880.5342 EKtot = 45282.2773 EPtot =
-215162.8116
BOND = 1202.0393 ANGLE = 3117.5743 DIHED =
4379.2958
1-4 NB = 1444.0330 1-4 EEL = 18190.9633 VDWAALS =
26857.0568
EELEC = -270353.7741 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 20792.9564 VIRIAL = 18931.2336 VOLUME =
738326.9432
Density =
0.9935
------------------------------------------------------------------------------
wrapping first mol.: 32.919882014605847 46.555742208107716
80.636904382153162
NSTEP = 4000 TIME(PS) = 15108.000 TEMP(K) = 308.77 PRESS =
118.9
Etot = -169465.7780 EKtot = 45352.2695 EPtot =
-214818.0475
BOND = 1243.8890 ANGLE = 3165.2093 DIHED =
4343.7269
1-4 NB = 1454.2485 1-4 EEL = 18147.6385 VDWAALS =
26847.8829
EELEC = -270020.6426 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 20831.6695 VIRIAL = 18927.3772 VOLUME =
741505.2239
Density =
0.9892
------------------------------------------------------------------------------
wrapping first mol.: 32.984081946003222 46.646534619046292
80.794161438151519
NSTEP = 5000 TIME(PS) = 15110.000 TEMP(K) = 309.77 PRESS =
8.0
Etot = -169124.4158 EKtot = 45500.3008 EPtot =
-214624.7166
BOND = 1232.2125 ANGLE = 3186.2957 DIHED =
4373.0240
1-4 NB = 1441.4137 1-4 EEL = 18166.4997 VDWAALS =
26912.3666
EELEC = -269936.5287 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 20850.4926 VIRIAL = 20722.4110 VOLUME =
745855.6038
Density =
0.9835
------------------------------------------------------------------------------
wrapping first mol.: 33.025442908005573 46.705027850693277
80.895474679087656
NSTEP = 6000 TIME(PS) = 15112.000 TEMP(K) = 308.71 PRESS =
-12.6
Etot = -168970.8114 EKtot = 45343.6445 EPtot =
-214314.4559
BOND = 1215.2167 ANGLE = 3100.9563 DIHED =
4394.4192
1-4 NB = 1442.5742 1-4 EEL = 18162.6633 VDWAALS =
26511.7142
EELEC = -269141.9998 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 20814.0035 VIRIAL = 21017.2944 VOLUME =
748665.6449
Density =
0.9798
------------------------------------------------------------------------------
wrapping first mol.: 33.086967987168919 46.792037449439590
81.046179712701829
NSTEP = 7000 TIME(PS) = 15114.000 TEMP(K) = 309.65 PRESS =
-4.8
Etot = -168696.3050 EKtot = 45481.4492 EPtot =
-214177.7542
BOND = 1190.8417 ANGLE = 3216.1231 DIHED =
4393.7839
1-4 NB = 1456.8171 1-4 EEL = 18157.1242 VDWAALS =
26497.1004
EELEC = -269089.5447 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 20804.6421 VIRIAL = 20882.5915 VOLUME =
752857.3860
Density =
0.9743
------------------------------------------------------------------------------
wrapping first mol.: 33.152543571133990 46.884775326837328
81.206806415180310
NSTEP = 8000 TIME(PS) = 15116.000 TEMP(K) = 308.96 PRESS =
185.1
Etot = -168821.5895 EKtot = 45380.1406 EPtot =
-214201.7302
BOND = 1189.9526 ANGLE = 3181.3004 DIHED =
4460.5056
1-4 NB = 1457.4336 1-4 EEL = 18168.8270 VDWAALS =
27180.8455
EELEC = -269840.5949 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 20873.1423 VIRIAL = 17846.8201 VOLUME =
757336.1500
Density =
0.9685
------------------------------------------------------------------------------
wrapping first mol.: 33.210338086428123 46.966509111724328
81.348373471877025
NSTEP = 9000 TIME(PS) = 15118.000 TEMP(K) = 307.23 PRESS =
-77.3
Etot = -168453.6000 EKtot = 45127.0664 EPtot =
-213580.6664
BOND = 1192.3988 ANGLE = 3234.5613 DIHED =
4438.5052
1-4 NB = 1491.9280 1-4 EEL = 18202.8854 VDWAALS =
26353.5548
EELEC = -268494.5000 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 20681.3967 VIRIAL = 21951.3281 VOLUME =
761312.7369
Density =
0.9635
------------------------------------------------------------------------------
wrapping first mol.: 33.249671128625003 47.022134431765572
81.444719344601964
NSTEP = 10000 TIME(PS) = 15120.000 TEMP(K) = 309.00 PRESS =
113.6
Etot = -167942.7414 EKtot = 45387.1953 EPtot =
-213329.9367
BOND = 1225.0005 ANGLE = 3179.3548 DIHED =
4433.6596
1-4 NB = 1462.4075 1-4 EEL = 18134.2929 VDWAALS =
26781.4190
EELEC = -268546.0709 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 20758.7465 VIRIAL = 18885.1763 VOLUME =
764014.4474
Density =
0.9601
------------------------------------------------------------------------------
*And before recompiling*
A V E R A G E S O V E R 6000000 S T E P S
NSTEP = 6000000 TIME(PS) = 15100.000 *TEMP(K) = 299.97* PRESS
= 0.9
Etot = -174591.2036 EKtot = 44060.5326 EPtot =
-218651.7362
BOND = 1182.5969 ANGLE = 3103.2954 DIHED =
4330.9094
1-4 NB = 1445.7690 1-4 EEL = 18247.2286 VDWAALS =
27507.8824
EELEC = -274469.4179 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 19796.4790 VIRIAL = 19781.7985 VOLUME =
724683.5259
*Density =
1.0122*
Ewald error estimate: 0.4665E-04
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 6000000 TIME(PS) = 15100.000 *TEMP(K) = 1.10* PRESS =
94.5
Etot = 276.3982 EKtot = 161.4464 EPtot =
223.9908
BOND = 28.9355 ANGLE = 42.8630 DIHED =
24.5703
1-4 NB = 15.9612 1-4 EEL = 40.7665 VDWAALS =
219.1620
EELEC = 344.0308 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 108.5762 VIRIAL = 1477.2910 VOLUME =
573.9448
*Density =
0.0008*
2011/8/23 Dmitry Mukha <dvmukha.gmail.com>
> Thank you, Scott, your solution works. How does it affect the simulation?
>
> What I did was
> sed -i 's[gpu->sim.randomSteps =
> MAX_RANDOM_STEPS;[gpu->sim.randomSteps = MAX_RANDOM_STEPS / 4;[g'
> $AMBERHOME/src/pmemd/src/cuda/gpu.cpp
>
>
> 2011/8/22 Scott Le Grand <varelse2005.gmail.com>
>
>> Yes, try dividing by 4 on a 1 GB card. It ought to get just enough
>> room...
>>
>
> --
> Sincerely,
> Dmitry Mukha
> Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
>
--
Sincerely,
Dmitry Mukha
Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
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Received on Fri Aug 26 2011 - 10:00:06 PDT
