Hi David,
Thanks a lot for your guidance. The problem was that there were too many elements (35 each) in the IGR1, IGR2 arrays.
May I ask is there a command in Amber that can insert a number of molecules in a solvated protein box just like the insert-molecules command in Gromacs and packmol? I tried to treat my molecules as ions and use addions command. The molecules were added successfully and they are all placed outside of the solvated box and very far away from the protein.
Many thanks,
Ming
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Sunday, 7 March 2021 11:06 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] makeDIST_RST
On Sun, Mar 07, 2021, Ming Tang wrote:
>
>Thanks for the precious guidance. This what I want and the script was
>perfect. But I after 4000 steps the production run got this error:
>cudaMemcpy GpuBuffer::Download failed an illegal memory access was
>encountered. And there is not restrain in the output as below:
>
>wrapping first mol.: 30.51583 43.15591 74.74821
>wrapping first mol.: 30.51583 43.15591 74.74821
>
> NSTEP = 4000 TIME(PS) = 608.000 TEMP(K) = 308.07 PRESS = -237.6
> Etot = -153810.1794 EKtot = 36112.7344 EPtot = -189922.9138
> BOND = 578.5793 ANGLE = 1445.0337 DIHED = 2202.2790
> 1-4 NB = 687.3814 1-4 EEL = 7970.8282 VDWAALS = 24116.2997
> EELEC = -226923.3149 EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 17106.3674 VIRIAL = 20136.3763 VOLUME = 590645.1967
> Density = 0.9997
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
A zero restraint energy probably just means that all the restraints are
satisfied, that is, that the average distance being restrained is greater
than 1.8 Å.
>
>&rst iat=-1,-1,0
> r1=1.300000, r2=1.800000, r3=10.000000, r4=10.500000, rk2=20.000000, rk3=0.000000,
> IGR1(1)=2794,IGR1(2)=2795,IGR1(3)=2796,...
> IGR2(1)=2829,IGR2(2)=2830,IGR2(3)=2831,...
> nstep1=0, nstep2=0,
> &end
Since you set rk3=0, this is just a lower bound. That is fine if it what
you want.
> nstlim=2000000000,dt=0.002,
Debugging steps:
1. Since the restraints aren't doing anything anyway, run a short
simulation (say 10000 steps, not 2 billion!) and see if you still get the
crash.
2. Set iwrap=0 (you should be doing this anyway). It's certainly possible
that the restraints get confused when wrapping is going on.
3. If the problem seems to be with the restraints, try a test run with many
fewer elements in the IGR1, IGR2 arrays. It's not clear how big those
arrays are, but there may be some upper bound.
4. Try setting ntb=1, ntp=0 to see if there is something odd about pressure.
> ntpr=1000, ntwx=1000,ntwr=1000,iwrap=1,
Note that if this job actually ran, you would probably exhaust all disk
space: you are asking to dump a trajectory every 1000 steps, so you would
get 2000000000/1000 = 2 million frames in your trajectory file(!)
...good luck...dac
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Received on Tue Mar 09 2021 - 15:00:02 PST
