[gmx-users] segmentation fault after mdrun

Dear justin, As you suggested i have changed the coloumb type to PME and set pme_order to 5 as said in the mailing list as it will increase the accuracy.But then the simulation is not getting completed.Its taking hours together.Normally what's the running time for a lipid bilayer?I dint find anyt

[gmx-users] How to define new residue in GROMACS?

For example, I want to add GTP as residue current force field, and after that pdb2gmx will be able to recognize GTP molecule. At first, I created GTP.pdb: REMARK This PDB file is created by CS Chem3D REMARK COMPND Untitled-1.pdb HETATM1 C UNK 0 -0.561 0.002 -1.145 C H

Re: [gmx-users] segmentation fault after mdrun

On Feb 23, 2009, at 9:22 AM, Nikit sharan wrote: Dear justin, As you suggested i have changed the coloumb type to PME and set pme_order to 5 as said in the mailing list as it will increase the Hi Nikit, I think pme_order should be an even number in gromacs. You might want to try with order =

Re: [gmx-users] Oscillating Electrical Field

Benjamin Hall wrote: Hi I'm trying to create an oscillating electrical field in my simulation, and I was hoping that someone who had successfully done this in the past could please offer some advice on the choice of parameters in my mdp. Eventually, I would like to create a system with oscill

Re: [gmx-users] How to define new residue in GROMACS?

Hi Yiming Chen, In this case there's no need to add GTP as a building block. Have a look at John Kerrigan's drug - enzyme tutorial to see how to include a prodrg topology in your simulation: http://wiki.gromacs.org/index.php/Tutorials Also, do note the caution regarding non-standard groups in yo

[gmx-users] MD parameters for DPPC bilayer

dear users, Can anyone send me the Md parameters(.mdp file) for dppc molecule with 12lipids and 3655 water molecules that worked without any errors like "pressure scaling not more than 1%" and more?It will be very helpful as i will check out that with my mdp file. Thanks in advance __

Re: [gmx-users] mdrun halting

varsha gautham wrote: Dear all, The production run of DPPC bilayer with 128 lipids and 3655 water and some solvent molecules is halting without completion.As justin suggested ,i changed the columb type from cut-off to PME.It keeps on running for hours together.The system is well equilibriated

Re: [gmx-users] segmentation fault after mdrun

Nikit sharan wrote: Dear justin, As you suggested i have changed the coloumb type to PME and set pme_order to 5 as said in the mailing list as it will increase the Try an even number. accuracy.But then the simulation is not getting completed.Its taking hours together.Normally what's the r

Re: [gmx-users] MD parameters for DPPC bilayer

Nikit sharan wrote: dear users, Can anyone send me the Md parameters(.mdp file) for dppc molecule with 12lipids and 3655 water molecules that worked without any errors like "pressure scaling not more than 1%" and more?It will be very helpful as i will check out that with my mdp file. Your p

[gmx-users] structure factor

Hello, I try to calculate structure factor for coarse-grained system with g_rdf, but I get error > Fatal error: > > Error: atom (B1) not in list (5 types checked)! It is possible to calculate structure factor for coarse-grained model with g_rdf? And how I can do it? Thanks in advance. ___

[gmx-users] protein structure prediction

can I use the GROMACS software to get the energy of a protein conformation? Up to now I am using TINKER library (analyze program). Is there any similar software in GROMACS? Thank you very much Best regards Jose Carlos -- José Carlos Calvo Tudela Miembro del Departamento de Arquitectura y Te

Re: [gmx-users] protein structure prediction

José Carlos Calvo Tudela wrote: can I use the GROMACS software to get the energy of a protein conformation? Yes, but your question is not well-formed. Only energy differences can have meaning. Up to now I am using TINKER library (analyze program). Is there any similar software in GROMACS?

Re: [gmx-users] protein structure prediction

So, In my software I make a pdb file with a certain conformation of the protein, then I need to know the energy of the conformation (CHARMM, AMBER,...), because I perform a minimization process. Is that possible? which program can do it in GROMACS? Thanks Jose Carlos Mark Abraham escribió:

Re: [gmx-users] protein structure prediction

23 feb 2009 kl. 12.55 skrev Mark Abraham: José Carlos Calvo Tudela wrote: can I use the GROMACS software to get the energy of a protein conformation? Yes, but your question is not well-formed. Only energy differences can have meaning. Up to now I am using TINKER library (analyze program

Re: [gmx-users] protein structure prediction

Per Larsson escribió: 23 feb 2009 kl. 12.55 skrev Mark Abraham: José Carlos Calvo Tudela wrote: can I use the GROMACS software to get the energy of a protein conformation? Yes, but your question is not well-formed. Only energy differences can have meaning. Up to now I am using TINKER lib

[gmx-users] About position restraint specification

Hello, all! Which option in .mdp file is used to specify position restraint and the corresponding force constant? -- Sun Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailma

Re: [gmx-users] About position restraint specification

Lee Soin wrote: Hello, all! Which option in .mdp file is used to specify position restraint and the corresponding force constant? In your topology, you should have something like: #ifdef POSRES #include "posre.itp" #endif The posre.itp file contains force constants; in the .mdp file you

Re: [gmx-users] About position restraint specification

There's also an option "freezegrps". When should this be used? 2009/2/23 Justin A. Lemkul > > > Lee Soin wrote: > >> Hello, all! >> Which option in .mdp file is used to specify position restraint and the >> corresponding force constant? >> >> > In your topology, you should have something like: >

Re: [gmx-users] About position restraint specification

Lee Soin wrote: There's also an option "freezegrps". When should this be used? Freeze groups: Manual section 3.3 Restraints: section 4.3 Note the fundamental difference between "fixed" and "harmonically restrained." -Justin 2009/2/23 Justin A. Lemkul mailto:jalem...@vt.edu>> Lee

[gmx-users] gromac running in ubantu 8.10

hello everybody i have install gromac in my ubantu8.10 through synaptic package but after install how to run the programme, where to put the input file ,how to run the programme. plz anybody help me. thank u have nice day -- akalabya N.I.T.Rourkela __

Re: [gmx-users] gromac running in ubantu 8.10

akalabya bissoyi wrote: hello everybody i have install gromac in my ubantu8.10 through synaptic package but after install how to run the programme, where to put the input file ,how to run the programme. 1. Read the manual. 2. Search Google for "Gromacs tutorial" 3. Visit wiki.gromacs.org

[gmx-users] Turning off electrostatic or Van der Waals interactions

Hi! Is there an option to turn off electrostatic or Van der Waals interactions in GROMACS? -- Sun Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Pl

Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

Lee Soin wrote: Hi! Is there an option to turn off electrostatic or Van der Waals interactions in GROMACS? Look into the free energy code; if this is not your intent, be more specific with what you are trying to do. -Justin -- Sun Li Department of Physics Nanjing University, China -

Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

I'm trying to rule out the effect of electrostatic or Van der Waals interactions while performing a simulation. Do you mean that I should modify the code and re-compile? 2009/2/23 Justin A. Lemkul > > > Lee Soin wrote: > >> Hi! >> Is there an option to turn off electrostatic or Van der Waals int

Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

Lee Soin wrote: I'm trying to rule out the effect of electrostatic or Van der Waals interactions while performing a simulation. Do you mean that I should modify the code and re-compile? No, I mean use the free energy options in the .mdp file. You may be able to use a B-state in the topol

[gmx-users] analysis using Gromacs tools

Dear All,   I'm planning to use Gromacs  for analysis with Amber trajectory files ( mdcrd, rst files ). And I found a script that converts Amber mdcrd files to Gromacs-compatible .xtc files. I want to learn that if Gromacs-compatible .xtc files are enough to perform an analysis using Gromacs too

[gmx-users] analysis using Gromacs tools

Dear All,   I want to use Gromacs  for analysis with Amber trajectory files ( mdcrd, rst files ). And I found a script ( trajectory_converter_v1.5.sh ) that converts Amber mdcrd files to Gromacs-compatible .xtc files. Does this script work well ? Also  I want to learn that if Gromacs-compatible

[gmx-users] analysis using Gromacs tools

You will require a .tpr file for many analysis tools. In some cases, you can get away with a .ndx file. Check g_thistool -h to see what is mandatory input. You can make a .ndx file if you have a .pdb using make_ndx -f my.pdb -o my.ndx and then select your groups. If you need a .tpr file, th

Re: [gmx-users] analysis using Gromacs tools

oguz gurbulak wrote: Dear All, I'm planning to use Gromacs for analysis with Amber trajectory files ( mdcrd, rst files ). And I found a script that converts Amber mdcrd files to *Gromacs-compatible .xtc *files. I want to learn that if *Gromacs-compatible .xtc *files are enough to perform

[gmx-users] Re: gmx-users Digest, Vol 58, Issue 125

plz anybody help me. > thank u have nice day > > -- > akalabya > N.I.T.Rourkela > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/15c5dae0/attachment-0001.html > >

[gmx-users] akalabya bissoyi has invited you to open a Google mail account

I've been using Gmail and thought you might like to try it out. Here's an invitation to create an account. --- akalabya bissoyi has invited you to open a free Gmail account. To accept this invitation and register for your accoun

Re: [gmx-users] Re: gmx-users Digest, Vol 58, Issue 125

e programme, where to put the input file ,how to run the programme. plz anybody help me. thank u have nice day -- akalabya N.I.T.Rourkela -- next part -- An HTML attachment was scrubbed... URL:

[gmx-users] obtaining gromacs for ubuntu (was Re: gmx-users Digest, Vol 58, Issue 125 (akalabya bissoyi))

Dear akalabya, First some general suggestions on using this mailing list: 1. Please pick a relevant title as your subject 2. Please don't include an entire digest in your post, it is irrelevant 3. Please take some more time to format your question. "plz help me" doesn't actually invoke a strong

[gmx-users] energy minimization with 4 nodes

Hi all, Is it right if running energy minimization using 4 nodes? thanks for any comment QIU YI HUAN ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www

Re: [gmx-users] energy minimization with 4 nodes

Q. Y. HUAN wrote: Hi all, Is it right if running energy minimization using 4 nodes? Yes. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/s

[gmx-users] energy minimization with 4 nodes

Hi all, Is it right if running energy minimization using 4 nodes? thanks for any comment QIU YI HUAN ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://ww

[gmx-users] Insertion of polymer into the bilayer

Dear all, I want to insert polymer in the aqueous phase of the bilayer.when i read through the mailing list i found that this can be done in three ways 1.By using genbox command genbox -cp polymer.pdb -cs bilayer.pdb -o merged.pdb this results in the insertion of polymer molecules to the centre

[gmx-users] energy minimization

Hi all, Is it right if running energy minimization using 4 nodes? thanks for any comments ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.o

Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

Why not create "dummy" topologies, without charges/vdw ? Another option, which I am not sure of its effect, is, perhaps, to take extremely small cutoffs. --Omer. > Lee Soin wrote: > >> I'm trying to rule out the effect of electrostatic or Van der Waals >> interactions while performing a simulatio

[gmx-users] make_hole

Dear all, When i look into the gromacs contributions couldnt locate mdrun_make_hole.tar.gz ..Is this a seperate file or is it coming with gromacs 3.14 only?it will be helpful if somebody send me a link to download mdrun_make_hole.tar.gz? -varsha ___ gmx

Re: [gmx-users] Insertion of polymer into the bilayer

varsha gautham wrote: Dear all, I want to insert polymer in the aqueous phase of the bilayer.when i read through the mailing list i found that this can be done in three ways 1.By using genbox command genbox -cp polymer.pdb -cs bilayer.pdb -o merged.pdb this results in the insertion of polymer

[gmx-users] (no subject)

Hi all, Is it right if running energy minimization using 4 nodes? thanks for any comment QIU YI HUAN ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://ww

Re: [gmx-users] make_hole

varsha gautham wrote: Dear all, When i look into the gromacs contributions couldnt locate mdrun_make_hole.tar.gz ..Is this a seperate file or is it coming with gromacs 3.14 only?it will be helpful if somebody send me a link to download mdrun_make_hole.tar.gz? I found the file in the GROMACS co