Hi Kirtana,
The *'s mean the value is too big to print in the space provided. In this
case your VDW energy is huge suggesting one of three things:
1) Your have a bad structure, atoms too close for example - what was the
final energy from the sander run?
2) Your restraint energy is also huge - perhaps you are restraining to an
innapropriate reference structure?
3) There is a bug in the code.
Firstly I am assuming you are running the minimization with the CPU
version of the code and then switching to the GPU version for the
dynamics? - If not then start by doing this. The SPFP precision model is
very intolerant of strained structures and thus I recommend that one
always minimizes with the CPU code.
For the dynamics set ntpr=1, nstlim=100, ntwx=1 - then run it and you will
be able to see what goes wrong at the beginning and visualize it. Note
tautp in your mdin file has no effect with ntt=3.
Finally check what version of the GPU code you are running (printed early
on in mdout) - make sure it is fully up to date. It should be 14.0 for
AMBER 14 and 12.3.1 for AMBER 12.
All the best
Ross
On 6/23/14, 8:40 AM, "kirtana S" <skirtana4.gmail.com> wrote:
>Dear Amber users,
>
>If I notice asteriosk or stars marks in my output file and restart file
> what does this imply. I had this job run in sander without any issues and
>noticed some error in pmemd cuda. I tried to rectify this by using iwrap 1
>and still notice similar result.
>I used mpi run and also single processor run.
>
>Can you tell me if the issue is with my input files or my starting
>structure. Minimization run was preformed on the solvent with restraint on
>solute before this step.
>My input file
>Minimization:
>&cntrl
> imin=1, ntx=1,
> dielc=1.0,ntmin=2,
> ntrx=1, ntxo=1,
> ntb=1,ioutfm=1,
> irest=0, cut=10.0,
> ntpr=1,
> maxcyc=10000,
> ntt=0, ntr=1,
>&end
>Hold the PRO fixed
>40.0
>RES 1 300
>END
>END
>
>Second step which give me the error
>
>&cntrl
> imin=0,ntx=1,
> cut=10.0,tempi=0.0,
> ntpr=100,ntwx=100,ntwe=100,
> nstlim=1000000,temp0=100.0,
> dt=0.001,
> ntc=2, ntf=2,
> irest=0,tautp=4.0,
> ntb=1,iwrap=1,
> ntt=3,gamma_ln=5.0,ntr=1,
> &end
>Hold surface fixed
>40.0
>RES 1 300
>END
>END
>
> NSTEP = 100 TIME(PS) = 0.100 TEMP(K) =********* PRESS =
>0.0
> Etot = ************** EKtot = ************** EPtot =
>**************
> BOND = -0.0000 ANGLE = 1580104.7120 DIHED =
>12738.0737
> 1-4 NB = 0.0000 1-4 EEL = -19.0698 VDWAALS =
>**************
> EELEC = -308.1300 EHBOND = 0.0000 RESTRAINT =
>**************
> EAMBER (non-restraint) = **************
>
>mden file
>
>L0 Nsteps time(ps) Etot EKinetic
>L1 Temp T_solute T_solv Pres_scal_solu
>L2 Pres_scal_solv BoxX BoxY BoxZ
>L3 volume pres_X pres_Y pres_Z
>L4 Pressure EKCoM_x EKCoM_y EKCoM_z
>L5 EKComTot VIRIAL_x VIRIAL_y VIRIAL_z
>L6 VIRIAL_tot E_pot E_vdw E_el
>L7 E_hbon E_bon E_angle E_dih
>L8 E_14vdw E_14el E_const E_pol
>L9 AV_permMoment AV_indMoment AV_totMoment Density
> dV/dlambda
>L0 100 0.1000000000E+00 0.2542518727E+16 0.2542508165E+16
>L1 0.3949644593E+14 0.3949644593E+14 0.2525519783E+22 0.1000000000E+01
>L2 0.1000000000E+01 0.1015340000E+03 0.1656810000E+03 0.3714600000E+02
>L3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
>L4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
>L5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
>L6 0.0000000000E+00 0.1056199933E+11 0.1970472220E+10 -.3081299803E+03
>L7 0.0000000000E+00 -.1024454832E-07 0.1580104712E+07 0.1273807373E+05
>L8 0.0000000000E+00 -.1906978498E+02 0.8589934592E+10 0.0000000000E+00
>L9 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
> 0.0000000000E+00
>
>Can you help me with this.
>
>Thanks
>Kirtana
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Received on Mon Jun 23 2014 - 13:30:02 PDT
