Hi Kirtana,
A few comments and suggestions here. Firstly using a restraint weight of
100 is probably way too high. I would reduce this to 5.0 or less. It may
be causing issues with the density equilibrating. Second if you are
simulating a protein, rather than a membrane, you should probably use
isotropic pressure scaling, ntp=1. The lack of coupling between the X, Y
and Z directions in anisotropic pressure scaling can sometimes lead to box
collapse in one dimension.
Thirdly make sure you are running with the latest version of the code.
What is being reported as the version number and date for the GPU code at
the beginning of your mdout file?
Finally your angle energy seems a little high to me and 348K is also a
very high temperature. I suspect something is very strained in your
initial structure. Check for overlaps or strange structures / bonds -
often creating a pdb and loading that into VMD so it bonds by distance can
be useful in detecting strange geometries by eye. Another issue like this
I have seen recently was with someone simulating a lipid membrane. They
set the initial box dimensions aggressively small and this resulting in
one of the alkane chains being forced through a ring. This causes huge
strain on the system and ultimately the simulation crashes. However it was
not obvious why because the clash was actually between 1 lipid tail and a
molecule in one of the image boxes - only when visualized with the
adjacent images shown did the problem become obvious.
I hope that helps.
All the best
Ross
On 7/2/14, 11:52 AM, "kirtana S" <skirtana4.gmail.com> wrote:
>Dear Amber Users,
>
>I am using pmemd.cuda single processor job run. In my equilibration step
>where I want to bring my system to the required density I am using ntb=2,
>ntp=2, pres0=1, taup=1.0 with time step 0.001 . After certian initial
>steps
>my output files give NaN in TEMP and sometime the energy is very high. I
>have set temp0 and tempi as 300K and temperature fluctuates a lot.
>
>So I used a a very small time step dt=0.0002, my job runs to certain
>extent
>and again stops . There is no error message in output file but there are
>some message as below. Can you help me with where I might be making a
>mistake here.
>
>Thanks Kirtana
>
>Nonbond cells need to be recalculated, restart simulation from previous
>checkpoi
>nt
>with a higher value for skinnb.
>sleeping
> ... finished
>
> NSTEP = 10100 TIME(PS) = 1100.520 TEMP(K) = 348.27 PRESS =
> -269.6
> Etot = -74527.3948 EKtot = 39082.0938 EPtot =
>-113609.4885
> BOND = 32717.8694 ANGLE = 11701.8297 DIHED =
>0.0000
> 1-4 NB = -3244.6814 1-4 EEL = -2704.0479 VDWAALS =
> 7789.3074
> EELEC = -165781.7780 EHBOND = 0.0000 RESTRAINT =
> 5912.0123
> EAMBER (non-restraint) = -119521.5008
> EKCMT = 14811.4565 VIRIAL = 19110.8720 VOLUME =
> 738482.1312
> Density =
>0.9585
>
>--------------------------------------------------------------------------
>----
>
>
> NSTEP = 10200 TIME(PS) = 1100.540 TEMP(K) = 345.40 PRESS =
> -217.4
> Etot = -74442.7865 EKtot = 38759.5820 EPtot =
>-113202.3685
> BOND = 32736.0643 ANGLE = 11538.8603 DIHED =
>0.0000
> 1-4 NB = -3246.0456 1-4 EEL = -2710.5924 VDWAALS =
> 8301.0357
> EELEC = -165989.5676 EHBOND = 0.0000 RESTRAINT =
> 6167.8768
> EAMBER (non-restraint) = -119370.2453
> EKCMT = 14671.2103 VIRIAL = 18137.5078 VOLUME =
> 738446.7256
> Density =
>0.9586
>
> &cntrl
> imin=0,
> ntxo=1, ntrx=1,
> cut=8.0, tempi=300.0, ntwprt=0,
> ntpr=100, ntwx=100, ntwe=100, ntwr=100, ioutfm=0,
> nstlim=100000, temp0=300.0,
> dt=0.0002, nscm=100,nsnb=10,dielc=1.0,
> ntc=2, ntf=2, tol=0.00001,
> ntx=5, irest=1,iwrap=1,
> ntb=2,ntp=2,pres0=1,taup=1.0,
> ntt=3,gamma_ln=2,ig=-1,
> ntr=1,restraintmask=':1-100',restraint_wt=100,
> &end
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Received on Wed Jul 02 2014 - 12:30:03 PDT
