Date: Mon, 17 Feb 2025 05:48:15 +0000
Thank you for your reply.
My work includes working on the protein aptamer complex where i am working on the 3HSB protein complex.
After addition of solvate box and minimization and heating the complex appears normal .as in figure 1, after running equilibration, at 1250000 steps, the water box breaks as well as the protein chains get distorted as in figure 2 and 3.
I have used autoimage and unwrap command but the issue doesn't seem to resolve.
I am using running the gpu cuda11.7
Below is the equilibration.in file I am using
&cntrl
imin=0, ntx=7, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
nscm=5000,
ntf=2, ntc=2,
ntb=2, ntp=1, tautp=0.2, taup=0.2,
nstlim=1250000, t=0.0, dt=0.002,
cut=9.0,
ntt=1,
ntr=1,
irest=1
&end
Group input for restraints: 0.5 kcal/mol.
40
RES 1 411
END
END
Please provide your valuable feedback and suggestion for solution
[cid:77cf0154-9954-4cac-ad29-5486c66e8a6d]
Figure 1
[cid:f6fcf3c0-1dee-42ad-9e5a-3de0ecdd08a5]
Figure 2
[cid:d14ba297-99c4-4eeb-97e8-b82ec15321f2]
Figure 3
________________________________
From: David A Case <dacase1.gmail.com>
Sent: 13 February 2025 20:11
To: TUSHAR GUPTA <E24SOEP0001.bennett.edu.in>
Subject: Re: [AMBER] Issue with Water Box Breaking in CUDA MD Simulations
On Thu, Feb 13, 2025, TUSHAR GUPTA wrote:
>
>I have run md1 and md2. md1 for 20ps and md2 for 100ps. After 20ps the
>water box starts to break. And even using the reimaging command the box
>still at the same condition.
Were you able to run the short CPU vs GPU tests that I suggested?
>Basically, you are getting different results from CPU and GPU. To start
>debugging, set up a short simulation (say 20 steps, with ntpr=1) and run
>twice, once with pmemd (not sander) and again with pmemd.cuda_DPFP. Look
>carefully at the two outputs to see what you can find.
The hope is that these short runs may help identify the reason for the
difference between pmemd and pmemd.cuda. I'm guessing that we are going to
need to see your files, but you should do this test yourself first.
....dac
“Your attitude, not your aptitude, will determine your altitude.” – Zig Ziglar
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