Hello Cristian,
Could you double check if you are using pmemd from Amber18? The CPIN file format changed in Amber18, when the flag PKA_CORR was added. If you use the option --old-format in your cpinutil.py command, it will generate the CPIN file in a format that is compatible with pmemd from Amber 16 or older versions.
I hope this helps,
Best,
Vinícius Wilian D. Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: cprivat.ub.edu <cprivat.ub.edu>
Sent: Monday, September 21, 2020 10:36 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] [CPHMD] invalid reference to variable in NAMELIST input, CPIN file
[External Email]
Hello,
I am running CpHMD simulations in AMBER18 (pmemd.cuda) and it crashes at the beginning of the production run. I have used a protocol (very similar to the one indicated by Jason Swails in his wikidot) that has worked on similar systems.
I have checked old messages of the mailing and I see that it has already been commented, but I hope that you can shed some light on the problem.
The specific error is: “Error: an illegal memory access was encountered launching kernel kNLSkinTest ”
I have done some tests:
- Run short simulations in NVT (and disactivated CPHMD) to relax the system before performing the production run.
- Change the thermostat (from Langevin to Berendsen), which seems to work. However, I would like to continue with the Langevin thermostat as it seems to work better for long simulations.
- Carry out the simulations on CPUs.
When using CPUs, I obtained the following error, which is more instructive:
forrtl: severe (19): invalid reference to variable in NAMELIST input, unit 23, file /scratch/1739534.1.iqtc06.q/asyn_2n0a_015_dyn.cpin, line 154, position 9
This line refers to “PKA_CORR=0.0000,4.0000,4.0000,4.0000,4.0000,10.4000,0.0000,0.0000,4.4000,4.4000,4.4000,4.4000,9.6000,0.0000,7.1000,0.6000,0.0000,” in the CPIN file.
I should add that the simulations are being carried out with hydrogen mass repartition (and dt=0.004). The protonation change attempt is done every 100 steps, and the water relaxation is set at 50 steps. I have performed simulations under these conditions using the same system (in another initial conformation) and they worked, so it seems that it shouldn't affect now.
So... in my opinion, it looks like a problem related with CPHMD. In fact, if I deactivate the method and perform the production run, the problem does not appear. Thus... I was wondering if you could give me some advice.
Thanks,
Cristian
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Received on Mon Sep 21 2020 - 09:00:02 PDT
