AW: velocity manipulation

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Oct 16 2014 - 08:26:37 CDT

Ok, as already pointed out, the *.vel files are simply pdb format and very easy to read. They contain velocity vectors for each atom. Please notice that _ONE_ *.vel file is only some kind of snaphot of the temperature distribution. It will give the target temperature in average for all particles but not for individual particles.

 

Do you need more information, please explain where you stuck.

 

Norman Geist.

 

Von: mostafa raeesi [mailto:mostafa.raesi_at_gmail.com]
Gesendet: Donnerstag, 16. Oktober 2014 15:19
An: Norman Geist
Betreff: Re: namd-l: velocity manipulation

 

Dear Sir,

I need to have the velocity of each atom to couple the outcome with another simulation i.e. DSMC.

 

On Thu, Oct 16, 2014 at 4:41 PM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:

Why do you want to do this?

 

Norman Geist.

 

Von: mostafa raeesi [mailto:mostafa.raesi_at_gmail.com]
Gesendet: Donnerstag, 16. Oktober 2014 14:58
An: Norman Geist
Betreff: Re: namd-l: velocity manipulation

 

Dear Norman,

Thank you for your swift response.

I want to manipulate velocity of atoms real time once every few steps. For this reason, I should have access to the velocity of each atom which to my knowledge is written on the non-binary file of (*.vel) and obviously is not of any use to me.

Please suggest if I can find them anywhere else.

Thanks in advance.

 

 

On Thu, Oct 16, 2014 at 3:57 PM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:

Hey,

 

a non-binary velocity file is simply PDB format ;)

But please notice that _ONE_ single velocity file doesn’t really tell anything. Regarding on what you try to analyze you could need a VELDCD. What are you going to do?

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von mostafa raeesi
Gesendet: Donnerstag, 16. Oktober 2014 13:37
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: velocity manipulation

 

Dear NAMD users,

I have difficulty reading the velocity file in non-binary format for my simulation results, please advise either an appropriate method e.g. a TCL code for the same or any features on NAMD (not VMD) that can be of assistance.

My appreciations,

Mostafa

 

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