[gmx-users] analysis the results of melocular dynamics simulation

[yp sun]

Dear Sir,
 
I finished my simulation with gromacs, but whatever orders I use to analysize the results, I always get errors. For example, when I type: 
g_density -f  md.trr
It returns: 

Program g_density, VERSION 3.3.1
Source code file: gmxfio.c, line: 706
Can not open file:
topol.tpr

When I type: 
 g_energy –f md.edr –o potential.xvg
It returns: 
Program g_energy, VERSION 3.3.1
Source code file: statutil.c, line: 799
Invalid command line argument:
–f

When I type:  g_rms –s md.tpr –f md.trr –o rmsd.xvg
 
It returns: 
Program g_rms, VERSION 3.3.1
Source code file: statutil.c, line: 799
Invalid command line argument:
–s
 
When I type: 
g_gyrate –f md.trr –s md.tpr –o gyrate.xvg
It retures: 
Program g_gyrate, VERSION 3.3.1
Source code file: statutil.c, line: 799
Invalid command line argument:
–f

I totally have no ideas about these error. I didn't get error information when I do the simulation. I should I do with this situation?
 
Thanks!
Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

--- 11年12月13日，周二, Tsjerk Wassenaar <tsjerkw at gmail.com> 写道：


发件人: Tsjerk Wassenaar <tsjerkw at gmail.com>
主题: Re: [gmx-users] How to neutralize 0.748e system charge
收件人: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
日期: 2011年12月13日,周二,下午7:22


Hi Sundar,

Just add 0.748 Cl-

But you might want to go back through your workflow and the topology
resulting from it, to see how you ended up with a non-integer charge.
It is sort of unphysical.

Cheers,

Tsjerk

On Tue, Dec 13, 2011 at 11:59 AM, Sundargenesan <sundargenesan at gmail.com> wrote:
> Dear GROMACS users,
>
>
> Total charge of my system:
>
> Including chain 1 in system: 2041 atoms 207 residues
>
> Including chain 2 in system: 2036 atoms 206 residues
>
> Including chain 3 in system: 44 atoms 1 residues
>
> Now there are 4121 atoms and 414 residues
>
> Total mass in system 46007.483 a.m.u.
>
> Total charge in system 0.748 e
>
>
>
> Is it possible to make charge in system zero and how?
>
>
> Thanks in advance for your reply
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111213/48f3ecc3/attachment.html>