[gmx-users] problem in ngmx

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 17 12:57:24 CEST 2009 


Ms. Aswathy S wrote:
> hi Justin,
> 
> I tried the NVT once with certain changes in the parameter file. Now its
> finished the 10 ps. But I have used the charge as the same from the
> antechamber program. Do you think the result will be reliable? Please check
> the mdp file attached for NVT.
> 

The .mdp file seems reasonable.  QM charges are not necessarily the end result 
in Gromos parameterization.  In fact, such calculations are often unnecessary. 
In my experience, assigning charges based on functional groups already present 
in the force field is often a reasonable starting point.  But in any case, you 
must always verify your results and, in the end, follow the same 
parameterization scheme as the original force field (which, in the case of the 
Gromos force fields, does not include QM charge calculations).

-Justin

> Thnaks for your help Aswathy Dept. Biotechnology Ext. 3108
> 
> ----- Original Message ----- From: "Justin A. Lemkul" <jalemkul at vt.edu> To:
> "Gromacs Users' List" <gmx-users at gromacs.org> Sent: Tuesday, June 16, 2009
> 5:29:46 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re:
> [gmx-users] problem in ngmx
> 
> 
> 
> Ms. Aswathy S wrote:
>> My point was I have set the NVT equilibration as 10 ps. But it run only 5.4
>>  ps. when I checked the temperature It was also stabilized at 5.4 ps. That
>> is why I went ahead with NPT.Can we consider OK, if the equilibration stops
>>  before the time we set??
>> 
> 
> Absolutely not.  If any MD process stops before it is supposed to, that means
> it crashed.
> 
>> I am following some literatures, from that i thought first I should 
>> equlibrate the water then  give restraint to water and equilibrate the 
>> protein further. thats why I did in that way???I will check that once
>> again.
>> 
> 
> Not necessary.  In all the recent literature I have seen, position restraints
>  are placed on the protein, while the solvent is free to move.  After some
> time, all restraints are removed and production MD is conducted.
> 
> In any case, your problem occurs before you get to this stage.  Your NVT is 
> failing; you need to figure out why.
> 
> -Justin
> 
>> 
>> Dept. Biotechnology Ext. 3108
>> 
>> ----- Original Message ----- From: "Justin A. Lemkul" <jalemkul at vt.edu> To:
>>  "Gromacs Users' List" <gmx-users at gromacs.org> Sent: Tuesday, June 16, 2009
>>  5:03:26 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: 
>> [gmx-users] problem in ngmx
>> 
>> 
>> 
>> Ms. Aswathy S wrote:
>>> sorry..forgot to attach the file...
>>> 
>>> After my NVT I have checked the PE of the system..It was stabilised..So I
>>>  thought everything was fine till NVT. How can i check whetehr its a
>>> problem with NVT?Is that the box type could be the resaon?
>>> 
>>> 
>> Convergence of PE is a good indicator that energy minimization is complete.
>>  The purpose of NVT is to stabilize the temperature of the system.  My main
>>  problem with what you said before was that you did 10 ps of NVT in 2600 
>> steps.  This seems wrong, given the fractional nature of the time step 
>> required to do such a procedure.  Use gmxcheck on the .trr or .edr file to 
>> see how many frames it finds; verify that you have a complete trajectory.
>> 
>> Also, in the .mdp file you attached, you are applying position restraints
>> to the water in your system.  If you are not also restraining the protein,
>> it is probably colliding with the water, causing the explosion you are
>> seeing. Why are you restraining water during NPT equilibration, or during
>> MD for that matter?
>> 
>> -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:
>>> Tuesday, June 16, 2009 4:44:47 PM GMT +05:30 Chennai, Kolkata, Mumbai,
>>> New Delhi Subject: Re: [gmx-users] problem in ngmx
>>> 
>>> 
>>> 
>>> 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 
>>>>>>> _______________________________________________ gmx-users mailing
>>>>>>>  list gmx-users at gromacs.org 
>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search
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>>>>>>> 
>>>>>>> 
>>>>> ------------------------------------------------------------------------
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________ gmx-users mailing
>>>>> list gmx-users at gromacs.org 
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
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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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