Hi Sunhee,
From the AMBER GPU page
http://ambermd.org/gpus/
Recommendation for Minimization
One limitation of the SPFP precision model is that force can be truncated if they overflow the fixed precision representation. This should never be a problem during MD simulations for any well behaved system. However, for minimization or very early in the heating phase it can present a problem. This is especially true if two atoms are close to each other and thus have large VDW repulsions. It is recommended therefore that for minimization you use the CPU version of the code. Only in situations where you are confident the structure is reasonable, for example if it was a snapshot from dynamics, should you use the GPU code (SPFP) for minimization.
If you still see the problem with the CPU code then it means your initial structure is bad in some way. Atom clashes, ring penetration etc.
All the best
Ross
> On Aug 11, 2016, at 6:25 PM, SUNHEE CHO <sunheecho2015.gmail.com> wrote:
>
> 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 - 19:00:02 PDT
