[gmx-users] pb with temperature in brownian dynamics

Sat Jun 30 20:55:03 CEST 2007

Hello everybody,

I have been starting using Gromacs (3.3.1) recently and I am facing some problems.
I am trying to simulate RNA with ffAMBER99, and I decided that a bd simulation
would be the most efficient. 
My problem is maybe a known/stupid one : the temperature used during the simulation
is twice the one I asked for with ref_t in my .mdp file. I can see it when runs are over 
with the option "Temperature" of g_energy, or simply by looking in energy.edr with gmxdump. There must be something wrong going on that I failed to understand.

Here is the relevant (?) paramaters of my .mdp :
constraints = all-bonds
constraint_algorithm = lincs
lincs_order = 8
integrator = bd
dt = 0.01 (or 0.002 or 0.1, I tried both)
bd_fric = 5000 (or 50000)
tcoupl = no 
tc-grps = System
tau_t = 0.1 (or 0.01, it should play no role anyway , should it ?)
ref_t = 310.0
pcoupl = no
gen_vel = yes
gen_temp = 310.0

coulomb_type = cutoff
vdwtype = cut-off
rcoulomb = 1.2
rvdw = 1.2
rlist = 1.2

My system is a  RNA + ffamber99 tip3p + NaCl. I did previous energy minimizations
that worked fine. I tried runs with different temperatures but the temperature of
the stimulation is always twice as big.
If anyone may help...Many thanks !

Michael Bon,
CEA, France

-------- Message d'origine--------
De: gmx-users-bounces at gromacs.org de la part de gmx-users-request at gromacs.org
Date: sam. 30/06/2007 12:00
À: gmx-users at gromacs.org
Objet : gmx-users Digest, Vol 38, Issue 84

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Today's Topics:

   1. Re: OpenMosix and Gromacs (Sabuj Pattanayek)
   2. Re: OpenMosix and Gromacs (Nicolas Sapay)
   3. Re: Re: error during the minimization (M.N. Manoj)
   4. center of mass (mahbubeh zarrabi)

----------------------------------------------------------------------

Message: 1
Date: Fri, 29 Jun 2007 17:18:03 -0500
From: Sabuj Pattanayek <sabuj.pattanayek at vanderbilt.edu>
Subject: Re: [gmx-users] OpenMosix and Gromacs
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4685851B.3090608 at vanderbilt.edu>
Content-Type: text/plain; charset=ISO-8859-1

My 0.02. Based on one of Moshe Bar's OpenMosix papers, Mosix increases
the performance of MPI processes by load balancing. However I would have
to say that this only works for compute bound processes. If there's
going to be lots of I/O between nodes Mosix won't do so well and may
very well degrade performance.

Did you run any benchmarks of NAMD + its parallel (CHARM?)
implementation vs NAMD + CHARM + Mosix? Does it help? Last I checked the
Mosix userland tools and some other key functionality still don't work
for 2.6 linux kernels.

Nicolas Sapay wrote:
> Hi everybody,
> 
> I wonder if someone has some experience with Gromacs and OpenMosix. Has
> someone tried recently to run Gromacs in parallel with an OpenMosix
> cluster? I have read some messages about that on the mailing-list but
> they have been posted several years ago... Things may have changed now.
> Additionally, I have  already used sucessfully NAMD and OpenMosix (but
> NAMD uses its own tool for parallel process).
> 
> Thanks
> 
> Nico
> 

------------------------------

Message: 2
Date: Fri, 29 Jun 2007 17:22:27 -0600
From: Nicolas Sapay <nsapay at ucalgary.ca>
Subject: Re: [gmx-users] OpenMosix and Gromacs
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <46859433.2090709 at ucalgary.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Actually, I have used OpenMosix some time ago in a another life :) All I 
remember is that NAMD was performing reasonably well as far as you 
didn't ask it to write coordinates every frames. It was handy to 
minimize/equilibrate a system or do some small computation like pressure 
profile. As far as I remember, I was able to compute something like 0.8 
ns/day on 10 proc for a system of 30~20000 atoms.

Nico

Sabuj Pattanayek wrote:
> My 0.02. Based on one of Moshe Bar's OpenMosix papers, Mosix increases
> the performance of MPI processes by load balancing. However I would have
> to say that this only works for compute bound processes. If there's
> going to be lots of I/O between nodes Mosix won't do so well and may
> very well degrade performance.
>
> Did you run any benchmarks of NAMD + its parallel (CHARM?)
> implementation vs NAMD + CHARM + Mosix? Does it help? Last I checked the
> Mosix userland tools and some other key functionality still don't work
> for 2.6 linux kernels.
>
> Nicolas Sapay wrote:
>   
>> Hi everybody,
>>
>> I wonder if someone has some experience with Gromacs and OpenMosix. Has
>> someone tried recently to run Gromacs in parallel with an OpenMosix
>> cluster? I have read some messages about that on the mailing-list but
>> they have been posted several years ago... Things may have changed now.
>> Additionally, I have  already used sucessfully NAMD and OpenMosix (but
>> NAMD uses its own tool for parallel process).
>>
>> Thanks
>>
>> Nico
>>
>>     
>
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>
>
>   

-- 
[ Nicolas SAPAY, Ph.D. ]
University of Calgary, Dept. of Biological Sciences
2500 University drive NW, Calgary AB, T2N 1N4, Canada
Tel: (403) 220-6869
Fax: (403) 289-9311

------------------------------

Message: 3
Date: Sat, 30 Jun 2007 10:34:27 +0530
From: "M.N. Manoj" <mnmanoj at gmail.com>
Subject: Re: [gmx-users] Re: error during the minimization
To: gmx-users at gromacs.org
Message-ID:
	<4eb2b0a50706292204s23009e10ufd94024a5ab64b4 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

We have used the free tool Argus Lab for geometry opt of the protein. For
small protein it will work, but u can try it. Use UFF & BFGS options. Did u
checked the Ramachandran plot of your protein?

Subject: Re: [gmx-users] Re: error during the minimization

thanks for your advice Mr. Manoj
I tried the same simulation by taking a structure which was already
minimized  by another software Amber. Using that structure as the starting
structure also, i got the same error i mention earlier.
please suggest me something
thanks

-- 
M.N. MANOJ
PROJECT LEADER - BIOINFORMATICS
VITTAL MALLYA SCIENTIFIC RESEARCH FOUNDATION
BANGALORE
INDIA
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Message: 4
Date: Sat, 30 Jun 2007 01:23:45 -0700 (PDT)
From: mahbubeh zarrabi <zarrab_m at yahoo.com>
Subject: [gmx-users] center of mass
To: gmx-users at gromacs.org
Message-ID: <20070630082345.66689.qmail at web51608.mail.re2.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1

Dear all
i want to determine the center of mass of my protein
in the z-dimension.which command in gromacs is useful
for me?
thanks

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