Re: [AMBER] makeDIST_RST

From: Ming Tang <m21.tang.qut.edu.au>
Date: Thu, 11 Mar 2021 01:39:08 +0000

Hi Daniel,

It worked for 29 heavy atoms in each group! Why do hydrogens make trouble?

thanks,
Ming
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Wednesday, 10 March 2021 9:36 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] makeDIST_RST

Try excluding hydrogens from the groups.

On Tue, Mar 9, 2021 at 5:51 PM Ming Tang <m21.tang.qut.edu.au> wrote:

> 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 .
>
> >
> >&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 Wed Mar 10 2021 - 18:00:02 PST
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