[gmx-users] Re: Re: Normal Mode limits for memory (fwd)

[David van der Spoel]

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

---------- Forwarded message ----------
Date: Sat, 7 Aug 2004 9:35:39 -0400
From: statk002 at fiu.edu
To: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: Re: Normal Mode limits for memory

Hello Dr.Spoel,
Thank you very much for your reply.I plan to submit by truncating the system and see if that works.Where can I get the potentials for truncated systems ?
Thanks
Sujit
PS : I have joined the subscription service.

> 
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Date: 2004/08/07 Sat AM 05:39:43 EDT
> To: statk002 at fiu.edu
> CC: gmx-users at gromacs.org
> Subject: Re: Normal Mode limits for memory
> 
> On Fri, 6 Aug 2004 statk002 at fiu.edu wrote:
> 
> >Hello Dr.Spoel
> >I am trying to run a NM simulkation but keep running into memory allocation problems.
> >
> >The code that I input is 
> >g_nmeig_d -f nm.mtx -s 1CF3_nm.tpr -o eigenvalue.xvg -v eigenvector.trr
> >
> >The error I get is : 
> >Reading frame       0 time    0.000   Dimensionality of matrix: 17454
> >Fatal error: calloc for hess (nelem=304642116, elsize=8, file gmx_nmeig.c, line 121): Cannot allocate memory
> You need 2.5 Gb memory for this operation. You could use a subset of your 
> system (only Ca for instance).
> >
> >Can you please gibe nay input in this regard ?
> >I dont have subscription to Gromacs user list and hence I had to mail you directly.
> Please subscribe then, and continue the discussion at the list.
> 
> 
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
>