[gmx-users] Re: combine two gro files

[shika]

Thanks Dr. Dallas for your replying.

But my friend told me that the extended one is only 2 ns not the total 22ns.

So,the gro for the extended one is not affect at all?

I thought that the gro file that prodice from the extend one is only 2 ns.

Thanks Doc!

On Wed, Mar 13, 2013 at 11:19 AM, Dallas Warren [via GROMACS]
<ml-node+s5086n5006280h64 at n6.nabble.com> wrote:
> Why is it that you want to combine the two coordinate files?
>
> md.gro is the coordinates of the system at the end of 20ns.
>
> md_extend.gro is the coordinates of the system at the end of 22ns.
>
> So combining them will not make much sense.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Discovery Biology
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> [hidden email]
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>> -----Original Message-----
>> From: [hidden email] [mailto:gmx-users-
>> [hidden email]] On Behalf Of Nur Syafiqah Abdul Ghani
>> Sent: Wednesday, 13 March 2013 2:10 PM
>> To: [hidden email]
>> Subject: [gmx-users] combine two gro files
>>
>> Hi all,
>>
>> I just finished my simulation protein in mix solvent with the file
>> name md.gro but when i analyze the protein it seems not stable yet
>> therefore i have to extend it about 2ns more.The previously i used
>> 20ns for my simulation.So the extended oneis name md_extend.gro and
>> also the others file, trr tpr.
>>
>> The command that i used to extend the simu is like below :
>> tpbconv -f md.trr -s md.tpr -o md_extend.tpr -extend 2000
>> mdrun -v -cpi md.cpt -deffnm md_extend
>>
>> >From what I understand the new file that created after extend is only
>> 2ns second.right?
>> How i can combine the gro file from the original and the extended one?
>> Because the xtc trr and also edr file i combine it by using comand
>> trjcat and eneconv.
>>
>> The trjcat cant combine the gro file because the error stated :
>> Fatal error:
>> Can not write a gro file without atom names
>>
>> So anyone facing this problems.?I already search in previous problem
>> but they said convert the gro to pdb?then use command cat..can i use
>> that?
>>
>> --
>> Best Regards,
>>
>> Nur Syafiqah Abdul Ghani,
>> Theoretical and Computational Chemistry Laboratory,
>> Department of Chemistry,
>> Faculty of Science,
>> Universiti Putra Malaysia,
>> 43400 Serdang,
>> Selangor.
>> alternative email : [hidden email]
>> --
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--
Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
alternative email : syafiqahabdulghani at gmail.com




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