[gmx-users] problem in ngmx

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 16 13:14:47 CEST 2009



Ms. Aswathy S wrote:
> Hi,
> 
> In my NPT step I think there is some poblem. i am getting the follo: error. I
> have used box as cubic I s that could be the problem???? Please see the
> md,..mop file
> 

You haven't posted the .mdp file.  In any case, see my previous message.  I 
think something went wrong during NVT.  Here, the messages indicate that your 
box is exploding.  See, for example:

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

-Justin

> Please try to hepl me.. Box[    2]={         nan,          nan,          nan}
>  Can not fix pbc. Warning: Only triclinic boxes with the first vector
> parallel to the x-axis and the second vector in the xy-plane are supported. 
> Box (3x3): Box[    0]={         nan,          nan,          nan} Box[    1]={
> nan,          nan,          nan} Box[    2]={         nan,          nan,
> nan} Can not fix pbc. Warning: Only triclinic boxes with the first vector
> parallel to the x-axis and the second vector in the xy-plane are supported. 
> Box (3x3): Box[    0]={         nan,          nan,          nan} Box[    1]={
> nan,          nan,          nan} Box[    2]={         nan,          nan,
> nan} Can not fix pbc. Warning: Only triclinic boxes with the first vector
> parallel to the x-axis and the second vector in the xy-plane are supported. 
> Box (3x3): Box[    0]={         nan,          nan,          nan} Box[    1]={
> nan,          nan,          nan} Box[    2]={         nan,          nan,
> nan} Can not fix pbc. Warning: Only triclinic boxes with the first vector
> parallel to the x-axis and the second vector in the xy-plane are supported. 
> Box (3x3): Box[    0]={         nan,          nan,          nan} Box[    1]={
> nan,          nan,          nan} Box[    2]={         nan,          nan,
> nan} Can not fix pbc.
> 
> ------------------------------------------------------- Program mdrun,
> VERSION 4.0.4 Source code file: nsgrid.c, line: 348
> 
> Fatal error: Number of grid cells is zero. Probably the system and box
> collapsed.
> 
> -------------------------------------------------------
> 
> "Would You Like to Be the Monster Tonight ?" (Captain Beefheart)
> 
> 
> OIn some pev Dept. Biotechnology Ext. 3108
> 
> ----- Original Message ----- From: "Ms. Aswathy S"
> <aswathys at amritapuri.amrita.edu> To: "Discussion list for GROMACS users"
> <gmx-users at gromacs.org> Sent: Tuesday, June 16, 2009 12:40:04 PM GMT +05:30
> Chennai, Kolkata, Mumbai, New Delhi Subject: Re: [gmx-users] problem in ngmx
> 
> 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 
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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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