[gmx-users] DPOSRES not working

[Sergio Manzetti]

I cant say I fancy one who wants make money on knowing what on other peoples mind, but that does not mean you are the same! :) 

I think this worked out, but what the "bug" may be, that after doing 5 simulations twice, each time the confout.gro is something different from the confout.gro that came out afterwards from using gmx trjconv maybe something irrelated and related to linux command line/rights etc? 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
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From: "Justin Lemkul" <jalemkul at vt.edu> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Thursday, September 7, 2017 3:02:10 PM 
Subject: Re: [gmx-users] DPOSRES not working 

On 9/7/17 8:52 AM, Sergio Manzetti wrote: 
> Hey Justin , you sound like Mark Zuckerberg :) 

I don't know whether that's good or bad... 

> Here is the command I used: 
> 
> gmx trjconv -f traj -o confout5000.gro -b 10000 -e 10000 

-dump 10000 is easier than using -b and -e, FYI. 

> 
> and it gives the write gro with DNA in the box as it should be. 

So then things worked, yes? 

> This confout.gro is not the same as came out from the GMX run, at the same moment as the TRJ and XTC came 

In what way? Why does this lead you to believe that your restraints 
aren't working? The questions I asked before are more diagnostic of 
whether or not things are functioning. Dumping a (non-PBC-corrected) 
frame and looking at another one (PBC corrected, albeit perhaps not in 
the best way) does not say anything about whether or not the algorithms 
are working. 

-Justin 

> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] 
> 
> 
> 
> From: "Justin Lemkul" <jalemkul at vt.edu> 
> To: "gmx-users" <gmx-users at gromacs.org> 
> Sent: Thursday, September 7, 2017 2:55:05 PM 
> Subject: Re: [gmx-users] DPOSRES not working 
> 
> On 9/7/17 8:45 AM, Sergio Manzetti wrote: 
>> It seems that GMX simply didn't write out the correct frame. The confout.gro file written out is written at the same time as the trajectories, and for some reason, this confout.gro file has nothing to do with the last output frame from the sims, when produced by gmx trjconv.. 
> confout.gro is the final frame, re-wrapped for PBC. So it may "look" 
> different from the final frame of the trajectory, but it's not. 
> 
> Unless you actually provide answers to the questions I asked and any 
> actual commands you're issuing (e.g. what did you do when you say 
> "produced by gmx trjconv" for instance?), then there's nothing anyone 
> here can do to help you. We can't see what you're seeing or interpret 
> what's in your mind :) 
> 
> -Justin 
> 
>> 
>> 
>> 
>> 
>> Sergio Manzetti 
>> 
>> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
>> 
>> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
>> Midtun 
>> 6894 Vangsnes 
>> Norge 
>> Org.nr. 911 659 654 
>> Tlf: +47 57695621 
>> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] 
>> 
>> 
>> 
>> From: "Justin Lemkul" <jalemkul at vt.edu> 
>> To: "gmx-users" <gmx-users at gromacs.org> 
>> Sent: Thursday, September 7, 2017 2:28:23 PM 
>> Subject: Re: [gmx-users] DPOSRES not working 
>> 
>> On 9/7/17 5:28 AM, Sergio Manzetti wrote: 
>>> Hi Johannes, yes, they are there in both cases: 
>>> 
>>> ; Include Position restraint file 
>>> #ifdef POSRES 
>>> #include "posre_DNA_chain_E.itp" 
>>> #endif 
>>> 
>> Do you have a position restraint energy term written in your .log file, 
>> and if so, what is its magnitude? Does your DNA start at the middle of 
>> the box (GROMACS convention) or at the coordinate origin (like other 
>> software)? If you watch the trajectory evolve, what happens? Does the 
>> DNA move a lot or does it just bounce back and forth around its original 
>> position (suggesting your box is simply too small and any time an atom 
>> crosses a boundary, you get a jump)? 
>> 
>> -Justin 
>> 

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

Justin A. Lemkul, Ph.D. 
Assistant Professor 
Virginia Tech Department of Biochemistry 

303 Engel Hall 
340 West Campus Dr. 
Blacksburg, VA 24061 

jalemkul at vt.edu | (540) 231-3129 
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html 

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