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?
Dept. Biotechnology Ext. 3108 ----- Original Message ----- From: "Justin A. Lemkul" <jalem...@vt.edu> To: "Discussion list for GROMACS users" <gmx-users@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" > <aswat...@amritapuri.amrita.edu> To: "Discussion list for GROMACS users" > <gmx-users@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" <jalem...@vt.edu> To: > "Discussion list for GROMACS users" <gmx-users@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" <jalem...@vt.edu> To: >> "Discussion list for GROMACS users" <gmx-users@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" <jalem...@vt.edu> >>> To: "Discussion list for GROMACS users" <gmx-users@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.ma...@gmail.com> To: "Discussion list for GROMACS users" >>>> <gmx-users@gromacs.org>, jalem...@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 < >>>> domm...@icp.uni-stuttgart.de > wrote: >>>> >>>> >>>> * Justin A. Lemkul < jalem...@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@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the >>>> archive at http://www.gromacs.org/search before posting! Please don't >>>> post (un)subscribe requests to the list. Use the www interface or send >>>> it to gmx-users-requ...@gromacs.org . Can't post? Read >>>> http://www.gromacs.org/mailing_lists/users.php >>>> >>>> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ gmx-users mailing list >> gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php > -- ======================================== 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 ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
md.mdp
Description: Binary data
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