(no subject)

From: Laura Tiessler (lauratiesslersala_at_gmail.com)
Date: Thu Jun 07 2018 - 06:24:00 CDT

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
# 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


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