[gmx-users] problem in ngmx

Ms. Aswathy S aswathys at amritapuri.amrita.edu
Tue Jun 16 09:10:04 CEST 2009 

hi justin,

your suggestions were helpful. Actually  charges in the ligand topology was having the problem. So I have added the charges from the antechamber. Did Energy minimization. Now did an NVT equilibration of 10 ps. It finished at 2600 steps. But shows reasonable Energy and Temperature (checked in the xmgrace). Seems it works fine..Now started the NPT equilibration. 

Thank you very much for your support.

Aswathy
Dept. Biotechnology
Ext. 3108

----- Original Message -----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Monday, June 15, 2009 4:58:20 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: Re: [gmx-users] problem in ngmx



Ms. Aswathy S wrote:
> Hi Justin,
> 
> Thanks for the reply.
> 
> Once again i tried to minimize the protein +ligand in vacuum. Also tried by 
> varying the maximum force constant. But that too converged at the 15 th step 
> (or lesser steps based on the Fmax). The em.mdp file i have attached here 
> with. Please go through that once please and tell me because of any of these 
> parameters, the system behaves odd??.
> 

As I said before, it is not the step that matters, it is whether or not the
system converges within your criteria.  I am assuming EM is working, based on
the fact that the process converges differently depending on different target
values for Fmax.  Your .mdp file looks reasonable.

If we can clarify for a moment - several messages ago you claimed that you were 
doing a 20-ps NVT equilibration that was finishing at 15 steps, but that appears 
to not be the case.  Is it the NVT step that is failing to complete?  Is ngmx 
failing to display the NVT trajectory, and did gmxcheck report problems with the 
.edr file?

> I think you are correct that the itp file created by PRODRG need corrections.
>  But how can I chek that is that the problem with that file or how can i 
> rectify?
> 

Parameterization is very difficult.  Prepare for a lot of advanced work.  Please 
see here:

http://oldwiki.gromacs.org/index.php/Parameterization

-Justin

> Dept. Biotechnology Ext. 3108
> 
> ----- Original Message ----- From: "Justin A. Lemkul" <jalemkul at vt.edu> To: 
> "Discussion list for GROMACS users" <gmx-users at gromacs.org> Sent: Sunday, 
> June 14, 2009 10:51:30 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi 
> Subject: Re: [gmx-users] problem in ngmx
> 
> 
> 
> Ms. Aswathy S wrote:
>> Hi Justin,
>> 
>> I tried maximum to find out the problem but i failed in that.
>> 
>> I will give you the detailed steps..Kindly check once and tell me where is 
>> the problem. As you suggested now i am trying in gromacs 4.0.4 . 1. The 
>> ligand topology file is generated in PRODRG beta server using the GROMOS 
>> 96.1 force field. 2. The protein toplogy file using gromos 96 43 a1 force 
>> field 3. Tried to minimize in vacuum (Please find the em.mdp file). But the
>>  cycle finished at 15 steps. But in some previous post I saw that its not
>> an error so I went ahead with genbox and further minimization. But ended in
>>  the same 15 th steps. also checked the gmxcheck for the files as you 
>> suggested it show the following error.
>> 
> 
> What is most important is not the number of steps necessarily, but that the 
> potential energy converged to an appropriate value and you reached an Fmax 
> below your target.
> 
> Realize that using a topology straight from PRODRG is often not the best 
> course. The charges and charge groups assigned by PRODRG often require manual
>  modification and verification of the parameters.  This could be a source of 
> problem.
> 
> It may be that there is some kind of bug, but before that can be proposed, 
> you have to demonstrate that the preparation steps were successful (i.e., EM 
> criteria of potential energy and Fmax).
> 
> -Justin
> 
>> '', 33685 atoms Last frame          0 time    1.000
>> 
>> Both files read correctly Checking energy file 1RBP_water_min.edr
>> 
>> 
>> ------------------------------------------------------- Program gmxcheck, 
>> VERSION 4.0.4 Source code file: enxio.c, line: 283
>> 
>> Fatal error: Energy file 1RBP_water_min.edr not recognized, maybe different
>>  CPU? -------------------------------------------------------
>> 
>> "I Do It All the Time" (Magnapop)
>> 
>> Am I doing any mistake in the steps???? Please find some time to help me.
>> 
>> 
>> 
>> Thank you very much, Aswathy Dept. Biotechnology Ext. 3108
>> 
>> ----- Original Message ----- From: "Justin A. Lemkul" <jalemkul at vt.edu> To:
>>  "Discussion list for GROMACS users" <gmx-users at gromacs.org> Sent:
>> Saturday, June 13, 2009 6:23:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, New
>> Delhi Subject: Re: [gmx-users] problem in ngmx
>> 
>> 
>> 
>> Ms. Aswathy S wrote:
>>> Thank you very much for the reply...
>>> 
>>> gmxcheck of my out shows a "segementation fault" in the last part. What 
>>> could be the problem??
>>> 
>>> this is the last part of the output
>>> 
>>> x[31416] (-7.37978e-03  6.79718e+00  6.07531e+00) - (-7.40000e-03 
>>> 6.79720e+00  6.07530e+00) x[31428] ( 2.35365e-01 -6.53947e-03 
>>> 5.65519e+00) - ( 2.35400e-01 -6.50000e-03  5.65520e+00) x[31478] ( 
>>> 1.54478e-02  6.14019e+00  5.74537e+00) - ( 1.54000e-02  6.14020e+00 
>>> 5.74540e+00) Segmentation fault
>>> 
>>> 
>>> The energy minimisation & the equilibration steps are finished at 15 step
>>>  eventhough it was given for 20 ps(10000 steps).But the output
>>> coordinates file doesnt show any abnornmality as i checked in the viewer?
>>> My equilibration step was in NVT.
>>> 
>>> whether nothing is happening or any other problem?
>>> 
>> If you got 15 steps when you expected 10000, it seems pretty clear to me 
>> that something crashed very early on in your simulation.
>> 
>> -Justin
>> 
>>> Thanks & regards, Aswathy
>>> 
>>> 
>>> 
>>> 
>>> Dept. Biotechnology Ext. 3108
>>> 
>>> ----- Original Message ----- From: "Manik Mayur" <manik.mayur at gmail.com>
>>>  To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>, 
>>> jalemkul at vt.edu Sent: Saturday, June 13, 2009 5:34:08 PM GMT +05:30 
>>> Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in 
>>> ngmx
>>> 
>>> 
>>> 
>>> 
>>> On Sat, Jun 13, 2009 at 5:14 PM, Florian Dommert < 
>>> dommert at icp.uni-stuttgart.de > wrote:
>>> 
>>> 
>>> * Justin A. Lemkul < jalemkul at vt.edu > [2009-06-13 07:31:17 -0400]:
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> Ms. Aswathy S wrote:
>>> 
>>> 
>>> Hi,
>>> 
>>> after equlibration of my protein and ligand I tried to create the energy 
>>> file ans well as the to display the trajectories using ngmx option,. But 
>>> it shows the follo: error,
>>> 
>>> Xlib: connection to ":0.0" refused by server Xlib: No protocol specified
>>> 
>>> 
>>> Can't connect to X Server. Check your DISPLAY environment variable
>>> 
>>> 
>>> Seems like your X environment is somehow not properly configured.
>>> 
>>> 
>>> If you are working through ssh, then you can :
>>> 
>>> $export DISPLAY=<your current computer's ip>:0.0
>>> 
>>> 
>>> 
>>> Or you are tunneling through a SSH connection. There are several 
>>> possiblities:
>>> 
>>> 1. Try ssh -X to login, this could solve the problem, if you are in 
>>> principle allowed to use X11 tunneling. 2. In case this does not work 
>>> either it can be that you are not allowed to tunnel X11.
>>> 
>>> However take care that you also need a properly configured XServer 
>>> running on your own system not just on the host you login. So in case you
>>>  use Windows or MacOS make sure this is the case.
>>> 
>>> Flo
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ************************************************
>>> 
>>> also the g_energy command shows that ,
>>> 
>>> Program g_energy_mpi, VERSION 3.3.3 Source code file: enxio.c, line: 239
>>> 
>>> 
>>> Fatal error: Energy file eq_2ps_ener.edr not recognized, maybe different 
>>> CPU?
>>> 
>>> 
>>> What does gmxcheck tell you about the file. Perhaps it has been corrupted
>>>  in some way.
>>> 
>>> Also, you may want to work with a more current version (4.0.5) to utilize
>>>  the newest features and bug fixes.
>>> 
>>> -Justin
>>> 
>>> 
>>> 
>>> 
>>> Can any one help me, please???
>>> 
>>> Thanks, Aswathy ASBT Dept. Biotechnology Ext. 3108 
>>> _______________________________________________ gmx-users mailing list 
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>>> 
> 
> 
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-- 
========================================

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

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