Re: Writing 3 subsequent timesteps to the DCD file

From: Mert Gür (
Date: Wed Apr 08 2009 - 04:44:09 CDT

Writing every 1 step gives me an huge DCD which is hard to handle even for
short simulation times.

How about I perform 3 simulations at the same time.

I have a previous simulation and I will use its restart files so that my
initial system conditions are specified.

1- First simulation I run with a DCD frequency of every 100th step

2-For the second simulation, I first run my simulation for 1 step and then
use the final restart files for my second simulation and get the DCD
frequency every 100th step

3--For the third simulation I first run my simulation for 2 step and then
use the final restart files for my third simulation and then get the DCD
frequency every 100th step.

So I need these simulations to be identically the same so that I will get
the consequent coordinates as I desire. In other words the 100. step of my
first simulation should be the 99. of the second and the 98. of the third.

As much as my understanding goes that should be possible. In case it is what
do I have to be carefull about?

Would it be enough if I set only the following parameters to 1?

nonbondedFreq 1
fullElectFrequency 1
stepspercycle 1


On Tue, Apr 7, 2009 at 2:24 PM, Mert Gür <> wrote:

> Hi everyone!
> I want to write the coordinates of 3 subsequent time frames into my DCD
> file.
> For example
> Lets say I have a DCD writing frequency of every 100th step. Hence I am
> writing the coordinates for the 100.time step and then for the 200.
> timestep......
> But what I need to do is to write my coordinates for the 100., 101, 102.
> timesteps and then for the 200., 201, 202. time step and then again for the
> 300., 301. ,302, timesteps and so on...
> Can I do that?
> Any suggestion or even alternative ways to do that would be of big help to
> me.
> Best,
> Mert
> Center for Computational Biology and Bioinformatics
> Koc University
> Sariyer 34450, Istanbul, Turkey

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