Re: [AMBER] cpptraj uses huge memory space while doing molsurf calculation

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 29 Oct 2015 12:46:58 -0600

Hi,

This is a strange error, especially since 'molsurf' shouldn't need
anywhere near that much memory for any reasonable # of atoms - for
example, for 34,686 atoms the memory requirement is about 168 MB.

My initial advice would be to run each 'molsurf' command separately to
see if it is one of them in particular that is causing the issue.
Also, you don't need to 'autoimage' prior to 'molsurf' (imaging has no
effect on the 'molsurf' calculation).

-Dan

On Wed, Oct 28, 2015 at 6:48 AM, anu chandra <anu80125.gmail.com> wrote:
> Hello,
>
> I am trying to do SASA calculation with molsurf module in CPPTRAJ in
> AmberTools 15. Unfortunately, the program got hanged with a sudden jump in
> memory usage from 1.5 GB to 30 GB of RAM and it showed the following
> message on the terminal,
>
> edge: 21883 v1: 22169 v2: 20158
> edge: 21892 v1: 20165 v2: 17260
> edge: 21894 v1: 22187 v2: 22054
> edge: 21896 v1: 22043 v2: 22188
> edge: 0 v1: 3 v2: 0
> edge: 3588 v1: 3951 v2: 3954
> edge: 21902 v1: 22197 v2: 20128
> edge: 21904 v1: 22191 v2: 22197
> edge: 21906 v1: 20132 v2: 22194
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): std::bad_alloc
>
>
>
> Below, please find the cpptraj input commands.
>
>
> **********************************************************
> trajin md1.crd
>
> autoimage
>
>
> molsurf d1 :1-505 out d1_SASA.dat probe 1.3
>
> molsurf d2 :1-201 out d2_SASA.dat probe 1.3
>
> molsurf d3 :202-407 out d3_SASA.dat probe 1.3
>
> molsurf d4 :408-505 out d4_SASA.dat probe 1.3
> ***************************************************************
>
> Please help me to figure out what went wrong with the calculation here.
>
> Many thanks
> Anu
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-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Oct 29 2015 - 12:00:03 PDT
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