Hi Sarah,
Can you clarify whether you see this with AMBER 12 with the latest bug
fixes please. That is your output file should contain the following:
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 12.3
|
| 04/24/2013
|
All the best
Ross
On 6/10/13 5:26 AM, "Sarah Graham" <sarahgra.umich.edu> wrote:
>Sorry if this is a repeat, my emails don't seem to be going through.
>
>Hi,
>
>I have been running MD simulations on a gpu and am having issues when
>restarting. I have ntt=2 and when restarting on gpu the first step has a
>temperature of about 2000 instead of 300. I have irest=1 and ntx=5 so
>velocity information should be read from the restart file. The restart
>files are there and have information in them. When I run the same
>simulations on cpu using the exact same input files the temperature does
>not spike like this. Has anyone seen this before or know what might be
>causing it? I am using Amber11 but I have also tried Amber12 and I still
>have the same issue.
>
>Thanks for your help,
>
>Sarah Graham
>
>
>input file
>
>Production run
> &cntrl
> imin = 0,
> irest = 1, ntx = 5,
> ntwe = 1000, ntwx = 1000, ntwr = 1000, ntpr = 1000, ntwv = 1000,
> ntt = 2, temp0 = 300.0, tempi = 300.0,
> dielc = 1, cut = 10.0,
> ntb = 2, ntp = 1, ntc = 2, ntf = 2,
> ig = -1,
> nstlim = 1250000, dt = 0.0020,
> /
>
>example output
>
>|-----------------------------
>----------------------
>Setting new random velocities at step 1000
>check COM velocity, temp: 0.004194 0.03(Removed)
>
> NSTEP = 1000 TIME(PS) = 69332.000 TEMP(K) = 1860.02 PRESS =
>-154.1
> Etot = 28134.4824 EKtot = 174025.4076 EPtot =
>-145890.9252
> BOND = 696.4149 ANGLE = 1824.4578 DIHED =
>2475.8020
> 1-4 NB = 833.1366 1-4 EEL = 8244.7069 VDWAALS =
>17977.2913
> EELEC = -177942.7347 EHBOND = 0.0000 RESTRAINT =
>0.0000
> EKCMT = 12792.8104 VIRIAL = 14330.6250 VOLUME =
>462044.0055
> Density =
>1.0133
>
>--------------------------------------------------------------------------
>----
>
>Setting new random velocities at step 2000
>check COM velocity, temp: 0.000951 0.00(Removed)
>
> NSTEP = 2000 TIME(PS) = 69334.000 TEMP(K) = 300.63 PRESS =
>-54.6
> Etot = -117857.7631 EKtot = 28126.8179 EPtot =
>-145984.5810
> BOND = 734.8103 ANGLE = 1823.5534 DIHED =
>2467.0220
> 1-4 NB = 852.7348 1-4 EEL = 8202.9194 VDWAALS =
>17875.8311
> EELEC = -177941.4521 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>203,2 1%
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Received on Mon Jun 10 2013 - 07:30:03 PDT
