Yan: [gmx-users] analysis tools

[Justin A. Lemkul]

Namd Namd wrote:
> 
> Dear Justin,
> 
> Well , I think that I can do it , can't I ? I have gromacs 4.0.7 and VMD 
> 1.8.7 . how can I make analysis using NAMD output files with these 

You can't do it with 4.0.7, only the 4.5.x series has the capability to use VMD 
libraries.  Your first message said you had 4.5.4 available.

> softwares ? Could you please give me more information about this 
> procedure ? What should I do ? Also ıs there a way to get a .tpr file 
> from namd top or psf files ?
> 

Not directly.  You'd either have to write a script to convert the topology to 
the right format (probably a lot of work) or follow a Gromacs tutorial to create 
the topology for your system.

http://www.gromacs.org/Documentation/Tutorials

-Justin

> Thanks in advance
> 
> ------------------------------------------------------------------------
> *Kimden:* Justin A. Lemkul <jalemkul at vt.edu>
> *Kime:* Namd Namd <namd_10 at yahoo.com>; Discussion list for GROMACS users 
> <gmx-users at gromacs.org>
> *Gönderildiği Tarih:* 6 Eylül 2011 15:17 Salı
> *Konu:* Re: [gmx-users] analysis tools
> 
> 
> 
> Namd Namd wrote:
>  > Dear All,
>  >
>  > I’m a new NAMD user and use NAMD and VMD for simulations. I want to 
> ask a question about trajectory analysis. I examined the gromacs 4.5.4 
> tools for making analysis and decided to use some of them for my NAMD 
> output files. Is there a way to convert my namd output files into 
> gromacs 4.5.4 outputs and use gromacs 4.5.4  analysis tools ?
>  >
>  > I will be very happy if you inform me about this issue.
>  >
> 
> Gromacs tools can read any trajectory format that VMD can read, provided 
> you have the VMD libraries available.  That said, many analysis tools 
> still require a .tpr file, which means you need a Gromacs topology of 
> your system so you can assemble this input.
> 
> -Justin
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================