Re: simultaneous simulation for protein in water and SMD

From: amit banerjee (
Date: Thu Oct 03 2013 - 12:36:23 CDT

Dear Dr. Axel Kohlmeyer,                    Thanks for your valuable suggestion. The issue here is not to cheat physics rather finding out some way using the configuration file (if at all exists) other than using GPU or multiple CPU to make the calculations little faster. And faster here do not mean accepting anything which provides wrong output or by any means compromising the true results . Reducing time cannot be done with the cost of true results. The question here is whether in a single quad core system is it possible to run two simulations simultaneously? Anyways, thanks for your reply. Regards, Amit                              ________________________________ From: Axel Kohlmeyer <> To: amit banerjee <> Cc: namd-l <> Sent: Thursday, October 3, 2013 5:39 PM Subject: Re: namd-l: simultaneous simulation for protein in water and SMD On Thu, Oct 3, 2013 at 2:33 PM, amit banerjee <> wrote: > Dear Friends, >                    I have a query regarding running simulation of a protein > in water and performing SMD concurrently. > Although, i  was able to run individual simulation, first protein in water > sphere/water box followed by SMD. > Both the simulation was tested in quad core linux and windows system > successfully. For  1ns simulation it took long time for each case. > I would like to know in a quad core single system (linux/windows) is it > possible concurrently running both the simulations, i.e.,  protein in water > and SMD,  by altering the configuration file. > My objective is to shorten the time period for overall simulations. you cannot cheat physics. well, not unless you are a rare genius. what use is to have results faster, if they are incorrect? so the only way to get your work done correctly and faster is to get hold of more CPUs. NAMD parallelizes very well and there are plenty of parallel compute resources. it only takes some effort to get hold of them. axel. > > Any helpful suggestion will be appreciated, suggestions with some .conf file > in this regard will be additionally helpful for me. > > looking forward for your suggestions. > > Amit K. Banerjee > Indian Institute of Chemical Technology, > India. > > -- Dr. Axel Kohlmeyer International Centre for Theoretical Physics, Trieste. Italy.

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