[gmx-users] Constraintes

Hi all gmx-users I am trying to constraintes some special bonds in em.mdp file for energy minimization. But I dont know how can I do it. Please help me. Thank you Mohamad ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Constraintes

Mohammad Ghahramanpour wrote: Hi all gmx-users I am trying to constraintes some special bonds in em.mdp file for energy minimization. But I dont know how can I do it. You will need to read about constraints and restraints in chapters 4 and 5 of the GROMACS manual. Mark

[gmx-users] Hello

I am carrying out energy minimization of the protein peptide complex. But even after using nstcomm=1 and/or pbc=xyz, my energy minimized structure has peptide far away from the binding site. This did not happen with ATP-protein complex. Even in Drug-enzyme tutorial, similar .mdp file is given

Re: [gmx-users] Hello

I am turning pbc =xyz as written in earlier correspondence. But in spite of this when i run g_rms after simulation, my initial structure itself shows ~1.5 nm rmsd. So is it a problem at g_rms stage or it is the problem related to PBC and really the peptide is flying off ?? Regards, Nikhil

Re: [gmx-users] Hello

nikhil damle wrote: I am turning pbc =xyz as written in earlier correspondence. But in spite of this when i run g_rms after simulation, my initial structure itself shows ~1.5 nm rmsd. So? You need to compare that with pre-simulation... So is it a problem at g_rms stage or it is the problem

RE: [gmx-users] Re: Problems with non-bonded interactions using OPLSAA

Hi, There is surely no problem with the gen-pairs option, as that would cause serious trouble with nearly all simulations performed with Gromacs. gen-pairs only sets the generation of pair parameters, not of the actual pair interactions in the topology. I have no clue to what it going wrong in

Re: [gmx-users] Hello

So the problem is that .tpr file has peptide shifted in another box as after g_rms with -pbc option, RMSD is still ~1.5A = .tpr file generated from .mdp file during grompp programme, has peptide away from its usual position. I am giving pbc = xyz in .mdp file as well. Why then .tpr file should

[gmx-users] GridMat MD Plot

Hi ALL, I ran a membrane simulation and for analysis I came across the GridMat MD software. However I am not able to plot the output values (Z values of a 20x20 matrix) as given in http://bevanlab.biochem.vt.edu/GridMAT-MD/examples.html . In my system Xmatrix is not working and I am trying to

[gmx-users] problem with the creating of a top-file

Dear all, I have a problem with the creating of a top-file with grompp_d because the following error appeared: Fatal error: [ file spc.itp, line 32 ] Atom index (1) in settles out of bounds (1-0). This probably means that you have inserted topologie section settles in a part belonging to a

Re: [gmx-users] Re: Problems with non-bonded interactions using OPLSAA

Hi. I found the same behavior with both 3 (3.3.3) and 4 (4.0.5) versions on x86_64. What I found is : 1. gen-pair correctly generates the 1-4 parameters (verified with gmxdump -s topol.tpr) But with no [pairs] defined, 1-4 interactions are not calculated no matter what the scale factor

RE: [gmx-users] Re: Problems with non-bonded interactions using OPLSAA

Hi, Again, to avoid confusion: there are two (or three) completely separate parts to this issue in Gromacs. 1) The generation of the actual pair interactions in the [ pairs ] section in the topology (.top) file. pdb2gmx does this for you. If you write a topology by hand, you also have to add

Re: [gmx-users] problem with the creating of a top-file

On 07/14/09, Saskia Frenzel saskiafren...@gmx.de wrote: Dear all, I have a problem with the creating of a top-file with grompp_d because the following error appeared: Fatal error: [ file spc.itp, line 32 ] Atom index (1) in settles out of bounds (1-0). This probably means that you

Re: [gmx-users] GridMat MD Plot

Hi, We recently released version 1.0.2, which contains an accessory script for properly formatting the output data for GNUPlot. Please download the new version, read the documentation, and try again. -Justin Anirban Ghosh wrote: Hi ALL, I ran a membrane simulation and for analysis I

[gmx-users] Re: some monomers get bonds among them

Hi, Please keep all Gromacs-related correspondence on the gmx-users list. Gromacs ignores CONECT records when assigning bonds. You must define bonds in the .rtp files. -Justin Mohammad Ghahramanpour wrote: Hello Dear I thought you can draw your polymer (getting bonds between your

[gmx-users] About the mdrun err's information

Dear everyone, When I input the command:mdrun -v -deffnm em, some err happen and some information is as below: - Program mdrun, VERSION 3.3.3 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During

Re: [gmx-users] About the mdrun err's information

Aurum Bai wrote: Dear everyone, When I input the command:mdrun -v -deffnm em, some err happen and some information is as below: - Program mdrun, VERSION 3.3.3 Source code file: nsgrid.c, line: 226 Range checking error:

Re: [gmx-users] Re: Problems with non-bonded interactions using OPLSAA

Thanks for the clarification, that explains everything. Perhaps page 112 of the v4 manual could be updated too : generate pairs = no (the default, get 1-4 interactions from the pair list, when parameters are not present in the list give a warning and use zeros) or yes (generate 1-4 interactions

RE: [gmx-users] Re: Problems with non-bonded interactions using OPLSAA

Hi, I changed that part as well and also updated it for the fact that grompp in 4.0 never generates zero parameters, but always generates a fatal error when parameters are missing. Berk Date: Tue, 14 Jul 2009 14:21:49 +0200 Subject: Re: [gmx-users] Re: Problems with non-bonded interactions

[gmx-users] Re: GridMat MD Plot (Justin A. Lemkul)

Hi Justin, Thanks a lot Justin. It has solved my problem. Bye,  Anirban GhoshGrade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India Looking for local information? Find it on Yahoo! Local

[gmx-users] Re: Best way to handle linear rigid molecules.

Hi gmx users I am still having problems modelling small linear molecules. Following advice from the forum (see below), I tried to define CO2 using 2 dummy atoms (with averaged masses) which I placed in the same positions as my oxygen atoms. (This involves having to replicate coordinates

RE: [gmx-users] Re: Best way to handle linear rigid molecules.

Hi, This is quite wrong. Your normal atoms are virtual sites defined from the two masses (you did it the other way around). If you put the masses at the oxygen postitions (which gives an incorrect moment of intertia, so incorrect dynamics, but correct thermodynamics), then your coefficients are

[gmx-users] GridMatMD Result Interpretation

Hello Justin, I have a query regarding the interpretation of the results of GridMatMD. In your paper you have given the eg. of KALP-DPPC simulation. The colour index (blue to red) ranges from 2.5 to 4.5. Its the distance between the P atoms of DPPC in the top and bottom layers i.e. the Z

Re: [gmx-users] monomers

Other way to do it is to edit the spectbond.dat for serach the atoms that you want to bond. The same way that gromacs made the bond between the HEME and the HIS On Mon, Jul 13, 2009 at 6:27 PM, Jarol E. Molina hamolin...@gmail.comwrote: Hi all I need some monomers get bonds among them, but

[gmx-users] Molecular Modeling Workshop and Model(l)ing'09 in Erlangen, Germany

Dear list subscribers, this year, the Molecular Modeling Workshop in Erlangen (formerly known as Darmstadt workshop) takes place Sunday 6th - Monday 7th September 2009 as a satellite meeting to Model(l)ing'09, an international conference on occasion to Tim Clark's 60th birthday. As every year,

Re: [gmx-users] GridMatMD Result Interpretation

Hi, To understand the figure, you should refer to ref. 12 in the GridMAT-MD paper (the original KALP-DPPC simulations by Kandasamy and Larson), which we used as a benchmark in developing the program, as well as the explanation in our Results section. The purpose of the rainbow gradient is

[gmx-users] Problem compiling gromacs-4.0.5 against mvapich2-1.4rc1

Hello all, I have built MVAPICH2-1.4rc1 with Infiniband support on a CentOS 5.3 box and am trying to build gromacs-4.0.5 with MPI support. make is failing with the following error message: mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -std=gnu99 -o

RE: [gmx-users] gromacs on glacier

Hi Justin, Regarding your suggestion using spc216, when I tried the energetically minimize spc216 with grompp,I got the following error: Program grompp, VERSION 4.0.4 Source code file: topio.c, line: 415 Fatal error: Syntax error - File spce.itp, line 1 Last line read: '[ moleculetype ]'

Re: [gmx-users] gromacs on glacier

Payman Pirzadeh wrote: Hi Justin, Regarding your suggestion using spc216, when I tried the energetically minimize spc216 with grompp,I got the following error: Program grompp, VERSION 4.0.4 Source code file: topio.c, line: 415 Fatal error: Syntax error - File spce.itp, line 1 Last line

[gmx-users] making a box of water

Hello, I am trying to make a box of water from three different water models. I can make one from my own water model, but when I want to test TIP4P and SPCE, as soon as it comes to energy minimization step and using grompp, I get the following error message: Program grompp, VERSION 4.0.4

Re: [gmx-users] making a box of water

Payman Pirzadeh wrote: Hello, I am trying to make a box of water from three different water models. I can make one from my own water model, but when I want to test TIP4P and SPCE, as soon as it comes to energy minimization step and using grompp, I get the following error message:

RE: [gmx-users] making a box of water

Here is my .top file: ;This includes SPC-E potential #include spce.itp [ system ] Pure box of water [ molecules ] SOL 515 I used the same thing with my own model, but it had worked. Payman -Original Message- From: gmx-users-boun...@gromacs.org

Re: [gmx-users] making a box of water

You need to #include an appropriate force field that contains the [defaults], [atomtypes], etc. before you can define a [moleculetype]. -Justin Payman Pirzadeh wrote: Here is my .top file: ;This includes SPC-E potential #include spce.itp [ system ] Pure box of water [ molecules ] SOL

RE: [gmx-users] making a box of water

Will #include ffgmx.itp solve my problem? Would it be a general solution or in each case I should specify (if I add other solutes such as proteins)? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: