[AMBER] Glycoprotein MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest

From: zizhang sheng <shengzizhang.gmail.com>
Date: Tue, 7 Jan 2020 10:47:45 -0500

Hi All,

When I run MD for glycoproteins in Amber18 pmemed.cuda.MPI, it always crash with the memory error when heating from 0k to 300k. The simulations without glycans but with identical MD parameters are all good. The glycan I added is MAN3 from Glycam. Tleap did not show any error. I also tried with the vlimit=20 option suggested in previous threads but run into the same error. I also tried with pmem.cuda and pmem.MPI, they all give the same error. The GPU card is 1080Ti. I wonder if anyone has the similar issue when simulating glycoprotein.

The steps I am running are:
1) minimize the solution
2) minimize the whole system
3) heating
4) equilibration

Attached is the parameters for heating.


Zizhang Sheng

nstlim=2500000, dt=0.002, ntx=1, irest=0, ntpr=20000, ntwr=20000, ntwx=20000,
tempi =0.0, temp0=300.0, ntt=3, gamma_ln=1.0,taup=5,
ntb=1, ntp=0,
ntc=2, ntf=2,
nrespa=1,!frequency of steps to evaluate slowly-varying terms

&wt type='TEMP0', istep1=0, istep2=900000, value1=0.0, value2=300.0 /
&wt type='TEMP0', istep1=900001, istep2=2500000, value1=300.0, value2=300.0 /
&wt type='END’ /
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Received on Tue Jan 07 2020 - 08:00:02 PST
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