Re: [gmx-users] RMSD plot

2012-07-30 Thread tarak karmakar
Dear Mark, Thanks for the reply. But one thing I am just wondering is that while calculating the RMSD, I'm considering the backbone only. So I can take the initial pdb file as reference for the trajectory. While doing so I see the RMSD graph is continuing to increase and not getting equilibrium

Re: [gmx-users] RMSD plot

2012-07-30 Thread Mark Abraham
On 30/07/2012 4:49 PM, tarak karmakar wrote: Dear Mark, Thanks for the reply. But one thing I am just wondering is that while calculating the RMSD, I'm considering the backbone only. So I can take the initial pdb file as reference for the trajectory. While doing so I see the RMSD graph is

[gmx-users] RE: gmx-users Digest, Vol 99, Issue 113

2012-07-30 Thread Du Jiangfeng (BIOCH)
Dear Mark, Thank you for your reply. I have read the documentations from http://www.gromacs.org/Documentation/Installation_Instructions/GPUs and also, from gromacs manual. I configured my system strictly followed by the instruction from it. My GPU is GTX-480, which is supported by gromacs.

[gmx-users] RE: Re: Help of mdrun-gpu (Mark Abraham)

2012-07-30 Thread Du Jiangfeng (BIOCH)
Dear Mark, Thank you for your reply. I have read the documentations from http://www.gromacs.org/Documentation/Installation_Instructions/GPUs and also, from gromacs manual. I configured my system strictly followed by the instruction from it. My GPU is GTX-480, which is supported by gromacs.

Re: [gmx-users] Diagnosing + system blowing up

2012-07-30 Thread Shima Arasteh
Thanks dear Mark. Actually the atomtype C is more suitable for C atom of formyl and not CT1! The same as before I get the no default bonds/angles/dihedral errors . You explained what I am suppose.  I can understand the way of matching the coordinate file and atom types in .rtp file. But it's

Re: [gmx-users] Diagnosing + system blowing up

2012-07-30 Thread Mark Abraham
On 30/07/2012 6:36 PM, Shima Arasteh wrote: Thanks dear Mark. Actually the atomtype C is more suitable for C atom of formyl and not CT1! The same as before I get the no default bonds/angles/dihedral errors . You explained what I am suppose. I can understand the way of matching the coordinate

[gmx-users] Gromacs installation

2012-07-30 Thread rama david
Hi GROMACS FRIENDS, I have dell T3500 precision, 64 bits, 6C workstation with fedora operating system. I want to install gromacs in parallel mode with mpi... I am planning to performed Replica Exchange Molecular Dynamics ( REMD ). As per REMD instruction

Re: [gmx-users] Gromacs installation

2012-07-30 Thread Linus Östberg
If you install package 1 on your list, the second one will be installed as well (ie you need both of them). // Linus On Mon, Jul 30, 2012 at 10:56 AM, rama david ramadavidgr...@gmail.com wrote: Hi GROMACS FRIENDS, I have dell T3500 precision, 64 bits, 6C workstation with fedora

Re: [gmx-users] Diagnosing + system blowing up

2012-07-30 Thread Shima Arasteh
In CHARMM36 folder, there is a atomtypes.atp that I chose the atomtypes of formyl group ( as you see earlier) . If I don't use these, so what atom types?! I sent an email to Prof.Roux the author of this article http://www.pnas.org/content/101/1/117.abstract . He suggested me to use the

Re: [gmx-users] Gromacs installation

2012-07-30 Thread Mark Abraham
On 30/07/2012 6:56 PM, rama david wrote: Hi GROMACS FRIENDS, I have dell T3500 precision, 64 bits, 6C workstation with fedora operating system. I want to install gromacs in parallel mode with mpi... I am planning to performed Replica Exchange Molecular Dynamics ( REMD ). As per REMD

Re: [gmx-users] Diagnosing + system blowing up

2012-07-30 Thread Mark Abraham
On 30/07/2012 7:11 PM, Shima Arasteh wrote: In CHARMM36 folder, there is a atomtypes.atp that I chose the atomtypes of formyl group ( as you see earlier) No, I saw atom types chosen that included wrong things like CT1. If you're happy that you're using atom types that belong in formyl, then

Re: [gmx-users] Diagnosing + system blowing up

2012-07-30 Thread Shima Arasteh
 You are right, CT1 is incorrect for sure. But the other option is C(carbonyl C) . Maybe I couldn't say it clearly. The FVAL which I sent before through mailing list, is the result of this formamide and the CGenff generation: [ FVAL ]     [ atoms ]         CN    C    0.357    0         ON   

Re: [gmx-users] Diagnosing + system blowing up

2012-07-30 Thread Mark Abraham
On 30/07/2012 7:41 PM, Shima Arasteh wrote: You are right, CT1 is incorrect for sure. But the other option is C(carbonyl C) . Maybe I couldn't say it clearly. The FVAL which I sent before through mailing list, is the result of this formamide and the CGenff generation: [ FVAL ] [

[gmx-users] a problem using g_sgangle

2012-07-30 Thread Za Pour
Dear gmx users I am trying to analyze the results of my simulations. a system including one CNT+12 small molecules.I would like to know the distribution of angles formed by  these 12 small molecules around CNT.I have found from manual that g_sgangle may do that however, in the manual has been

Re: [gmx-users] a problem using g_sgangle

2012-07-30 Thread Justin Lemkul
On 7/30/12 5:55 AM, Za Pour wrote: Dear gmx users I am trying to analyze the results of my simulations. a system including one CNT+12 small molecules.I would like to know the distribution of angles formed by these 12 small molecules around CNT.I have found from manual that g_sgangle may do

Re: [gmx-users] Gromacs installation

2012-07-30 Thread rama david
thank you for immediate reply... Suppose, If I installed from Fedora software packages How to check that Gromacs installed in Parallel version and can performed REMD Thank you in Advance.. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Diagnosing + system blowing up

2012-07-30 Thread Shima Arasteh
  If you want further help, you will need to paste your .rtp entry(s), the N-terminal fragment of your pdb2gmx -f input, pdb2gmx command line, full pdb2gmx output, the N-terminal fragment of the grompp -c input, grompp command line, and full grompp output. You may think your context is clear,

Re: [gmx-users] Gromacs installation

2012-07-30 Thread Mark Abraham
On 30/07/2012 8:34 PM, rama david wrote: thank you for immediate reply... Suppose, If I installed from Fedora software packages How to check that Gromacs installed in Parallel version and can performed REMD Make topol0.tpr and topol1.tpr as copies of the same .tpr file, and run mpirun

Re: [gmx-users] Gromacs installation

2012-07-30 Thread rama david
Thank you M.ark.. I got following reply.. Fatal error : mdrun -multi is not supported with thread library .Please compile gromacs with MPI support. I have to try to compile gromacs as per the webpage instructions... With best wishes and regards.. Rama David.. -- gmx-users mailing list

Re: [gmx-users] Diagnosing + system blowing up

2012-07-30 Thread Mark Abraham
On 30/07/2012 8:49 PM, Shima Arasteh wrote: If you want further help, you will need to paste your .rtp entry(s), the N-terminal fragment of your pdb2gmx -f input, pdb2gmx command line, full pdb2gmx output, the N-terminal fragment of the grompp -c input, grompp command line, and full

[gmx-users] About EM Error (simulation exploding)

2012-07-30 Thread vidhya sankar
Dear Justin, Thank you for your Previous Reply. I have got the following Error in EM using steepest Descent method in   gromacs Warning: 1-4 interaction between 4728 and 4733 at distance 3.030 which is larger than the 1-4 table size 3.000 nm These are ignored for the rest

[gmx-users] Linear Interaction energy calculations

2012-07-30 Thread sai nitin
Dear all, I recently started protein ligand simulation using gromacs my aim is to calculate binding free energies after simulations...I adapted justin tutorial and done 10 ns MD simulations using CHARMM FF and now going through LIE (Linear Interaction Energie method) g_lie in gromacs.. And came

Re: [gmx-users] Diagnosing + system blowing up

2012-07-30 Thread Shima Arasteh
Wow!  That was a fabulous explanation given to me. Thanks dear Mark! :-) I regenerated the topol.top to check the correctness of input and FF files. Some output has been changed however a little bit. Now, I bring you all was needed again: 1. rtp entry [ FVAL ]  [ atoms ]     CN    C    

Re: [gmx-users] About EM Error (simulation exploding)

2012-07-30 Thread Justin Lemkul
On 7/30/12 1:07 PM, vidhya sankar wrote: Dear Justin, Thank you for your Previous Reply. I have got the following Error in EM using steepest Descent method in gromacs Warning: 1-4 interaction between 4728 and 4733 at distance 3.030 which is larger than the 1-4 table

Re: [gmx-users] Linear Interaction energy calculations

2012-07-30 Thread Justin Lemkul
On 7/30/12 5:15 PM, sai nitin wrote: Dear all, I recently started protein ligand simulation using gromacs my aim is to calculate binding free energies after simulations...I adapted justin tutorial and done 10 ns MD simulations using CHARMM FF and now going through LIE (Linear Interaction

Re: [gmx-users] Diagnosing + system blowing up

2012-07-30 Thread Mark Abraham
On 31/07/2012 7:16 AM, Shima Arasteh wrote: Wow! That was a fabulous explanation given to me. Thanks dear Mark! :-) I regenerated the topol.top to check the correctness of input and FF files. Some output has been changed however a little bit. Now, I bring you all was needed again: 1. rtp

Re: [gmx-users] Diagnosing + system blowing up

2012-07-30 Thread Shima Arasteh
I edited the grompp output and sent it to you. Bring that again here:   Generated 21528 of the 21528 non-bonded parameter combinations  Generating 1-4 interactions: fudge = 1  Generated 18355 of the 21528 1-4 parameter combinations  ERROR 1 [file topol.top, line 414]:       No default Bond types