Re:

From: Laura Tiessler (lauratiesslersala_at_gmail.com)
Date: Thu Jun 14 2018 - 13:38:28 CDT

Hi David,
I have taken out the part that doubles the patches, but I have got the same
memory problem.
Do you know what else could be causing this problem?

Thank you in advance

2018-06-07 21:18 GMT+02:00 David Hardy <dhardy_at_ks.uiuc.edu>:

> What is the "patch problem" that you are trying to avoid by doubling the
> number of patches in each dimension? Since this doubling in each dimension
> actually increases the number of patches by a factor of 8, doing so could
> be the cause of the out-of-memory error that you are experiencing.
>
> --
> David J. Hardy, Ph.D.
> Beckman Institute
> University of Illinois at Urbana-Champaign
> <https://maps.google.com/?q=Champaign+405+N.+Mathews+Ave.,+Urbana,+IL+61801&entry=gmail&source=g>
> 405 N. Mathews Ave., Urbana, IL 61801
> <https://maps.google.com/?q=Champaign+405+N.+Mathews+Ave.,+Urbana,+IL+61801&entry=gmail&source=g>
> dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/
>
> On Jun 7, 2018, at 6:24 AM, Laura Tiessler <lauratiesslersala_at_gmail.com>
> wrote:
>
> Hi all,
> running MD using NAMD version: NAMD/2.12-CrayIntel-17.08-cuda-8.0 on a
> system of about 44 millions atoms (proteins in explicit water).
> At the stage of the first minimization, I got this memory problem:
> Reason: Could not malloc()--are we out of memory?
>
> I am using structure and coordinates in binary format, and this the input
> file:
> #
> # Input Namd Configuration File.
> # Protein Minimization.
> #
>
> # molecular system
> usePluginIO yes
> structure ionized.js
> bincoordinates ionized.coor
>
> # force field
> paratypecharmm on
> parameters ./par_all36_prot.prm
> parameters ./par_all36_na.prm
> parameters ./toppar_water_ions_namd.str
> exclude scaled1-4
> 1-4scaling 1.0
>
> # Doubling the number of patches (trying to avoid patch problem)
> twoAwayX yes
> twoAwayY yes
> twoAwayZ yes
> # approximations
> switching on
> switchdist 10
> cutoff 12
> pairlistdist 13.5
>
> # constraints
> constraints on
> conskfile restraint.pdb
> conskcol B
> consref ionized.pdb
>
> # output files
> binaryoutput yes
> noPatchesOnOne yes
> outputname min_solv_namd.md
>
> # run minimization
> minimization on
> minimize 500
>
>
> Does anyone have suggestions how could I solve the memory problems? Anyone
> that worked with large systems >10millions
>
> thanks
> regards
>
>
>

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