Hi
I have a problem on minimization process
I am trying to do minimization process with large protein which has 2334
residues
I got RESTARTED DUE TO LINMIN FAILURE error
detail I attached the out log
I am using pemed.cuda with titan 124 GB memory (for the memory is okay to
run)
about 1,400,000 water molecules were added to this system during tleap
also I added Na+ ions to make the system neutral
*********************************
My input file for explicit minimization.
min1: initial minimization by fixing the solute
&cntrl
imin = 1,
maxcyc = 1000,
ncyc = 500,
ntb = 1,
cut = 8,
ntr = 1
/
Hold the protein fixed
500.0
RES 1 2334
END
END
********************************
*******************************
out file
no numbers for 1-4 VDW etc
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.2086E+09 1.2793E+02 3.3644E+04 CD1 32137
BOND = 14439.9445 ANGLE = 355.3580 DIHED =
0.0000
VDWAALS = ************* EEL = ************* HBOND =
0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -2.9227E+09 7.3940E+01 2.5364E+04 CD1 4166
BOND = 31766.4552 ANGLE = 745.1880 DIHED =
0.0000
VDWAALS = ************* EEL = ************* HBOND =
0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -1.4190E+07 8.6520E+00 1.6469E+04 N 25134
BOND = 808599.4976 ANGLE = 2648.6568 DIHED =
0.0000
VDWAALS = 1492553.4659 EEL = ************* HBOND =
0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
150 -1.5093E+07 4.1032E+00 4.0875E+03 CD 25129
BOND = 839753.9014 ANGLE = 1221.5396 DIHED =
0.0000
VDWAALS = 1517375.9929 EEL = ************* HBOND =
0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
200 -1.5436E+07 3.0157E+00 3.9938E+03 CD 25129
BOND = 864292.9287 ANGLE = 978.8121 DIHED =
0.0000
VDWAALS = 1572458.0791 EEL = ************* HBOND =
0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
0.0000
************************************************
for the vacuum minimization is okay to run.
no error, all fine I think
********* out for vacuum********
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.9395E+14 3.9345E+13 5.5447E+15 CB 36609
BOND = 7184.0382 ANGLE = 4393.6416 DIHED =
26253.4721
VDWAALS = ************* EEL = -158471.2565 HBOND =
0.0000
1-4 VDW = 5770294.9209 1-4 EEL = 99284.5407 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
5 4.1590E+13 5.9097E+12 6.8272E+14 CB 36609
BOND = 7184.1572 ANGLE = 4393.6933 DIHED =
26253.4597
VDWAALS = ************* EEL = -158459.6618 HBOND =
0.0000
1-4 VDW = 5770297.2404 1-4 EEL = 99284.5230 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
10 3.2590E+12 2.2414E+11 2.3494E+13 NE 5043
BOND = 7185.6493 ANGLE = 4394.4549 DIHED =
26253.4909
VDWAALS = ************* EEL = -158387.8919 HBOND =
0.0000
1-4 VDW = 5770413.5234 1-4 EEL = 99284.5779 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
15 1.2277E+11 4.5976E+09 3.4197E+11 NE 5043
BOND = 7196.4584 ANGLE = 4399.3576 DIHED =
26254.0987
VDWAALS = ************* EEL = -158279.3091 HBOND =
0.0000
1-4 VDW = 5780929.3109 1-4 EEL = 99285.0794 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
20 4.3597E+09 5.3542E+07 2.5648E+09 CD1 23957
BOND = 7304.0485 ANGLE = 4432.2240 DIHED =
26257.5025
VDWAALS = ************* EEL = -158238.2136 HBOND =
0.0000
1-4 VDW = 6923878.1935 1-4 EEL = 99284.0364 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
25 2.1052E+08 1.0939E+06 4.4864E+07 CZ 5045
BOND = 8220.5489 ANGLE = 4628.4524 DIHED =
26274.7337
VDWAALS = ************* EEL = -158265.6947 HBOND =
0.0000
1-4 VDW = 2336759.3857 1-4 EEL = 99282.3612 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
30 7.1191E+06 1.6310E+04 4.6536E+05 CE 32625
BOND = 14508.4342 ANGLE = 5979.7234 DIHED =
26390.6480
VDWAALS = 7091801.1897 EEL = -158175.5044 HBOND =
0.0000
1-4 VDW = 39287.1921 1-4 EEL = 99287.6149 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
35 2.8987E+05 2.3945E+02 1.7676E+04 CZ 13496
BOND = 44338.0650 ANGLE = 10951.0305 DIHED =
26815.9106
VDWAALS = 253939.8204 EEL = -158054.2533 HBOND =
0.0000
1-4 VDW = 12630.2759 1-4 EEL = 99253.3098 RESTRAINT =
0.0000
***************************************
However the GB and explicit minimization is weird.
as I attached they got no number for the 1-4 VDW etc..
Can you please give me any comments on this problem ?
Thanks you in advance.
Best,
Sunhee Cho
--
*Sunhee Cho*
Master Course
Nano/Bio Computational Chemistry Laboratory
Department of Chemistry
Sookmyung Women's Univerisity
Cheongpa-ro 47 gil 100, Yongsan-gu, Seoul, 04310, Korea
Tel. : +82-2-710-9410
Mobile : +82-10-7661-5896
Email : sunheecho2015.gmail.com
ᐧ
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Received on Thu Aug 11 2016 - 18:30:02 PDT
