Re: Fw: [gmx-users] trjconv in martini

2012-01-11 Thread mohammad agha
ou any > suggestion about my problem, please? > > Best Regards > Sara > > > > rom: Tsjerk Wassenaar > To: mohammad agha ; Discussion list for GROMACS users > > Sent: Wednesday, January 11, 2012 1:38 PM > > Subject: Re: Fw: [g

Re: Fw: [gmx-users] trjconv in martini

2012-01-11 Thread Tsjerk Wassenaar
ut my problem, please? > > Best Regards > Sara > > > > rom: Tsjerk Wassenaar > To: mohammad agha ; Discussion list for GROMACS users > > Sent: Wednesday, January 11, 2012 1:38 PM > > Subject: Re: Fw: [gmx-users] trjconv

Re: Fw: [gmx-users] trjconv in martini

2012-01-11 Thread mohammad agha
;, line 68, in >     o = open(sys.argv[2],"w") > IndexError: list index out of range > > May I ask you to help me, please? > > Best Regards > Sara > > From: Tsjerk Wassenaar > To: mohammad agha ; Discussion list for GROMACS

Re: Fw: [gmx-users] trjconv in martini

2012-01-11 Thread Tsjerk Wassenaar
>     o = open(sys.argv[2],"w") > IndexError: list index out of range > > May I ask you to help me, please? > > Best Regards > Sara > > From: Tsjerk Wassenaar > To: mohammad agha ; Discussion list for GROMACS users > >

Re: Fw: [gmx-users] trjconv in martini

2012-01-11 Thread mohammad agha
to help me, please? Best Regards Sara From: Tsjerk Wassenaar To: mohammad agha ; Discussion list for GROMACS users Sent: Wednesday, January 11, 2012 12:54 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, That can only happen if the input file is

Re: Fw: [gmx-users] trjconv in martini

2012-01-11 Thread Tsjerk Wassenaar
Tsjerk Wassenaar > To: mohammad agha ; Discussion list for GROMACS users > > Sent: Saturday, December 31, 2011 3:41 PM > > Subject: Re: Fw: [gmx-users] trjconv in martini > > Hi Sara, > >> # Extract the first part of the trajectory >> trjconv -s md.tpr -f md.trr

Fw: Fw: [gmx-users] trjconv in martini

2012-01-10 Thread mohammad agha
- Forwarded Message - From: mohammad agha To: "gmx-users@gromacs.org" Sent: Tuesday, January 10, 2012 9:08 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Tsjerk, I know that my question is silly but please help me. I installed python2.5 on my system,

Re: Fw: [gmx-users] trjconv in martini

2012-01-10 Thread mohammad agha
k you to help me, Please? Best Regards Sara From: Tsjerk Wassenaar To: mohammad agha ; Discussion list for GROMACS users Sent: Saturday, December 31, 2011 3:41 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, > # Extract the first part of the trajector

Re: Fw: [gmx-users] trjconv in martini

2011-12-31 Thread mohammad agha
Hi Tsjerk, Thank you very much from your help. Best Regards Sara From: Tsjerk Wassenaar To: mohammad agha ; Discussion list for GROMACS users Sent: Saturday, December 31, 2011 3:41 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, > # Extr

Re: Fw: [gmx-users] trjconv in martini

2011-12-31 Thread Tsjerk Wassenaar
Hi Sara, > # Extract the first part of the trajectory > trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 1 That should be -e 19 :) But you can also use -e 20. Probably that is better. I first thought it'd be better to avoid a double frame, but since trjcat is used to combine the

Re: Fw: [gmx-users] trjconv in martini

2011-12-31 Thread mohammad agha
ce again your workflow. I hope work this time. I thank you very very much again. Best Regards Sara From: Tsjerk Wassenaar To: mohammad agha ; Discussion list for GROMACS users Sent: Saturday, December 31, 2011 2:18 PM Subject: Re: Fw: [gmx-users] trjconv in mart

Re: Fw: [gmx-users] trjconv in martini

2011-12-31 Thread Tsjerk Wassenaar
agha ; Discussion list for GROMACS users > > Sent: Saturday, December 31, 2011 11:42 AM > Subject: Re: Fw: [gmx-users] trjconv in martini > > Hi Sara, > > Please find the script as attachment. When saved, you have to make it > executable using > > chmod +x xtcrev.py >

Re: Fw: [gmx-users] trjconv in martini

2011-12-31 Thread mohammad agha
#!/usr/bin/env python > May I ask you to help me? > > Best Regards > Sara > > > From: Tsjerk Wassenaar > To: mohammad agha ; Discussion list for GROMACS users > > Sent: Friday, December 30, 2011 8:06 PM > Subject: Re: Fw: [gmx-use

Re: Fw: [gmx-users] trjconv in martini

2011-12-31 Thread mohammad agha
Hi Tsjerk, Thanks for your reply, yas, I did this too! Best Regards Sara From: Tsjerk Wassenaar To: mohammad agha ; Discussion list for GROMACS users Sent: Saturday, December 31, 2011 11:42 AM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara

Re: Fw: [gmx-users] trjconv in martini

2011-12-31 Thread Tsjerk Wassenaar
n > May I ask you to help me? > > Best Regards > Sara > > > From: Tsjerk Wassenaar > To: mohammad agha ; Discussion list for GROMACS users > > Sent: Friday, December 30, 2011 8:06 PM > Subject: Re: Fw: [gmx-users] trjconv in martini

Re: Fw: [gmx-users] trjconv in martini

2011-12-30 Thread mohammad agha
-users] trjconv in martini Hi Sara, Make sure the first line of the script is: #!/usr/bin/env python Cheers, Tsjerk On Dec 30, 2011 1:25 PM, "mohammad agha" wrote: > > >- Forwarded Message - From: mohammad agha To: Tsjerk Wassenaar -- >gmx-users mailing list    gmx-u

Re: Fw: [gmx-users] trjconv in martini

2011-12-30 Thread Tsjerk Wassenaar
Hi Sara, Make sure the first line of the script is: #!/usr/bin/env python Cheers, Tsjerk On Dec 30, 2011 1:25 PM, "mohammad agha" wrote: - Forwarded Message - From: mohammad agha To: Tsjerk Wassenaar http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht

Fw: [gmx-users] trjconv in martini

2011-12-30 Thread mohammad agha
- Forwarded Message - From: mohammad agha To: Tsjerk Wassenaar Sent: Friday, December 30, 2011 3:16 PM Subject: Re: [gmx-users] trjconv in martini Hi Tsjerk, Thank you very much from your reply, I have a problem about ./xtcrev.py 1a.xtc > 1a-rev.xtcI did ./xtcrev.py 1a.xtc > 1a-r