[gmx-users] HPC mpi how to run batch system

I think thebatch system will be more efficient. Theinteractive mode is not good, because we have to wait for the job. So is there any program or do we have to write some small program to creat a batch jobs? Thanks Forwarding messages From: gromacs Date: 2010-12-15 09:42:0

[gmx-users] amber convert gromacs input files

Hi , I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam web(they are glycam06 force field,included in AMBER) , but cannot converted this amber files to gromacs files format. Can anyone help me to convert this (amber) files to gromacs input files(top or itp,gro).

Re: [gmx-users] PME or Reaction field suitable for Gromos forcefield ?

On 2010-12-22 22.57, Sanku M wrote: Thanks David for the response. I was going through the supporting material of your paper to understand the methodology . For G96 forcefield, you wrote 'For the gromos96 simulations marked “cutoff ” a reaction field with ǫ = 54 was applied beyond a cutoff of14

[gmx-users] Unknown bond_atomtype MNH3

Hello Justin, Thank you for your reply. I modifed ffG53a6bn_lipid.itp [ atomtypes ] ;name mass charge ptype c6 c12 ; LO15.99940.000 A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS LOM15.99940.000 A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS LNL14.00

Re: [gmx-users] Silly question?

Quoting Sergio Manzetti : > Thanks Justin: here is the top: > If this is the entire .top, it's missing several critical sections, and most notably you haven't #included a force field prior to defining your molecule. What you have is an .itp file, not a .top. -Justin > > [ moleculetype ] > ; Nam

[gmx-users] How to count the number of waters in the first hydration shell of a macromolecule

Dear users: I believe that the easiest way to calculate the number of water molecules in the first hydration shell of a macromolecule or molecular cluster is as follows. ## Set your cutoff as determined from g_rdf DIST=0.435 ## Calculate the data using g_mindist -respertime echo -e "SOL_OW

Re: [gmx-users] PME or Reaction field suitable for Gromos forcefield ?

Thanks David for the response. I was going through the supporting material of your paper to understand the methodology . For G96 forcefield, you wrote 'For the gromos96 simulations marked “cutoff ” a reaction field with ǫ = 54 was applied beyond a cutoff of14 Å, for the opls/aa “cutoff ” simulati

Re: [gmx-users] PME or Reaction field suitable for Gromos forcefield ?

On 2010-12-22 21.57, Sanku M wrote: *From:* Sanku M *To:* gmx-u...@gromacs.org *Sent:* Wed, December 22, 2010 1:06:09 PM *Subject:* PME of Reaction field for Gromos forcefield ? Hi, I was trying to use g53a5 gromos force

[gmx-users] PME or Reaction field suitable for Gromos forcefield ?

From: Sanku M To: gmx-u...@gromacs.org Sent: Wed, December 22, 2010 1:06:09 PM Subject: PME of Reaction field for Gromos forcefield ? Hi, I was trying to use g53a5 gromos forcefield for my study of protein in water . But, I found the original parameter

[gmx-users] interfacial water molecules

Part 1: Dear users, does anybody have a good method to calculate the number of water molecules in the first hydration shell of a macromolecule? Part 2: Dear Leila, My Oct 23 2010 comment was correct in intention and general ideas, but I was incorrect when I suggested that it would be easy

[gmx-users] Silly question?

That looks like a .itp file that you can include in your .top file. To see what a .top should look like, find a small peptide or protein and run it through pdb2gmx to get a .top file. You'll see that there is indeed a section of the .top that is like what you have here. Usually, one then st

Re: [gmx-users] Silly question?

Thanks Justin: here is the top: [ moleculetype ] ; Namenrexcl BZP 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1opls_648 1BZP C1 1 012.0107 ; qtot 0 2

Re: [gmx-users] Silly question?

Sergio Manzetti wrote: I am trying to grompp a molecule, but get the same error again: Program grompp, VERSION 4.5.1 Source code file: topio.c, line: 654 Fatal error: Syntax error - File bzp.itp, line 1 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype For more in

[gmx-users] Silly question?

I am trying to grompp a molecule, but get the same error again: Program grompp, VERSION 4.5.1 Source code file: topio.c, line: 654 Fatal error: Syntax error - File bzp.itp, line 1 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype For more information and tips for trouble

[gmx-users] deciphering the output of g_helixorient ?

Dear All I am trying to use g_helixorient to calculate the tilt of a peptide. This one is modeled with MARTINI. I am selecting all backbone atoms of the 23-residue peptide as my index group and am using g_helixorient as follows: g_helixorient -s peptide.tpr -f peptide.xtc -n peptide.ndx -otilt t

Re: [gmx-users] "Atomtype OW not found"

Justin A. Lemkul wrote: shikha agarwal wrote: I m doning membrane protein simulation , in POPE environment using this tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html when I run command: grompp -f minim.mdp -c pope.gro -p

Re: [gmx-users] "Atomtype OW not found"

shikha agarwal wrote: I m doning membrane protein simulation , in POPE environment using this tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html when I run command: grompp -f minim.mdp -c pope.gro -p topol_pope.top -o em.tpr I a

[gmx-users] "Atomtype OW not found"

I m doning membrane protein simulation , in POPE environment using this tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html when I run command: grompp -f minim.mdp -c pope.gro -p topol_pope.top -o em.tpr I always facing this error "A

Re: [gmx-users] atom type errer

mohsen ramezanpour wrote: Dear All I am using protein-drug binding. when I am using grompp this error occuring: Atomtype CR6 not found and Atomtype CR5 not found. by what can I replace these atom types? Looks like you're mixing and matching force fields. Is your drug topology from PRODRG?

[gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites

Dear Rossen: I'm pretty sure that my username used to be chris.ne...@utoronto.ca but when I tried to log in with that yesterday (first time in a while) it was unrecognized. I created the username cneale yesterday and that is the one that I will use. Thank you, Chris. -- original message

[gmx-users] atom type errer

Dear All I am using protein-drug binding. when I am using grompp this error occuring: Atomtype CR6 not found and Atomtype CR5 not found. by what can I replace these atom types? this is my drug.itp file: [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CR61 1

Re: [gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites

Hi, On 12/22/10 4:39 AM, Justin A. Lemkul wrote: chris.ne...@utoronto.ca wrote: Dear Roland: I am not sure what my barrier is electronically, only that there is a barrier. The web site has changed since my last attempt to make modifications, but I still can not add to the site as I once co

Re: [gmx-users] center the protein to the origin

Asmaa Elsheshiny wrote: Hi, I am simulating a protein in water. But I have forgotten to center the protein from the beginning to the origin. So, is it possible to center the When using periodic boundary conditions, the "center" of the system is an arbitrary designation. Gromacs builds boxes

[gmx-users] center the protein to the origin

Hi, I am simulating a protein in water. But I have forgotten to center the protein from the beginning to the origin. So, is it possible to center the protein to the origin in the trajectory file? And if it is not possible, how can obtain the atomic positions independent of the center of mass,

Re: [gmx-users] location of aminoacids.dat

First, please start a new thread if you are asking a new question. Hijacking an existing thread confuses the archive and will likely get your question ignored by anyone not interested in reading about Buckingham potentials. I have changed the subject line appropriately. See comments below.

Re: [gmx-users] adding Na and cl ions to pdb structure

mohsen ramezanpour wrote: Dear All How can I add one Na ion and cl ion to a pdb structure? for example I want to have a pdb file which contains my protein and one Na and one Cl ion. by pymol?How? by manipulating pdb file?How? If you want to place them in a known location, just write their

Re: [gmx-users] g-dist

mohsen ramezanpour wrote: Dear justin please check this part of my .gro file. ... 630VAL C 6416 0.554 11.700 -0.442 630VAL O1 6417 0.522 11.605 -0.534 630VAL O2 6418 0.534 11.834 -0.454 631<1> N2 1 2.686 2.399 2.151 631<1> C20 2 2.613

Re: [gmx-users] simulation of membrane protein

shikha agarwal wrote: Hi, I have a problem with Gromacs. I want to do MD simulations with my membrane proteïn in a POPE-membrane. Therefore I followed Justin Lemkul's tutorial on membrane proteïn simulation. I want to add ions. But when I use grompp to get a .tpr file for genion, Gromacs

Re: [gmx-users] stopping mdrun without error massage

Dear Karim, a (small) load imbalance is perfectly normal for a parallel simulation and no need to switch over to particle decomposition (both domain and particle decomposition should however work). Are you shure you get no error message? People will need some more information here to be able to he

[gmx-users] stopping mdrun without error massage

In God We Trust Hello Dear GMX users I want to do MD on one peptide in water with gromacs 4.5.3. I minimized and equilibrated my system in NPT and NVT for 50 ps , but when I do final mdrun it has load imbalance and when I try -pd option it stops after 265 ps without any error massage !, can ever

Re: [gmx-users] Re: gb_saltconc in implicit water simulations

Hi! Which results can you not recreate? Yes - all simulations were run at zero salt concentration. Implicitly this means that we did not do anything special to treat the charges. The protein has an overall charge of -2, looking at the topology. In hindsight, we probably should have given this i

Re: [gmx-users] simulation of membrane protein

On Wed, Dec 22, 2010 at 11:23 AM, shikha agarwal wrote: > I am trying to simulate a theorical model of a membrane protein in explicit > lipid bilayer membrane environment (DMPC or POPC), I have the pdb > files of this protein and membrane , I have to topolies files this > lipids (dmpc.

[gmx-users] simulation of membrane protein

Hi, I have a problem with Gromacs. I want to do MD simulations with my membrane proteïn in a POPE-membrane. Therefore I followed Justin Lemkul's tutorial on membrane proteïn simulation. I want to add ions. But when I use grompp to get a .tpr file for genion, Gromacs fives the following error: /

[gmx-users] simulation of membrane protein

I am trying to simulate a theorical model of a membrane protein in explicit lipid bilayer membrane environment (DMPC or POPC), I have the pdb files of this protein and membrane , I have to topolies files this lipids (dmpc.ip or popc.itp). How we can create merged topology of lipid an

[gmx-users] simulation of membrane protein

I am beginner in the GROMACS I am trying to simulate a theorical model of a membrane protein in explicit lipid bilayer membrane environment (DMPC or POPC), I have the pdb files of this protein and membrane , I have to topolies files this lipids (dmpc.ip or popc.itp). How we can create merged t

Re: [gmx-users] buckingham potentials

Dear Justin I hope all is well with you. I have faced a problem. I connect to imperial college london from my conunty to do the simulations. Today I faced an strange problem. every command wich I want to use for ex: g_msd_mpi or make_ndx_mpi  I get this fatal error: Fatal error: Library file amin

Re: [gmx-users] buckingham potentials

Dear justin, since i am rewritting a force field i am able to write the c6 and c12 parameter in force field file but how to do i declare the parameter B of bucking ham equation .Wat notation should i use for declaring it in force field file.The parameter C is declared as c6 and A

[gmx-users] adding Na and cl ions to pdb structure

Dear All How can I add one Na ion and cl ion to a pdb structure? for example I want to have a pdb file which contains my protein and one Na and one Cl ion. by pymol?How? by manipulating pdb file?How? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/ma

Re: [gmx-users] g-dist

Dear justin please check this part of my .gro file. ... 630VAL C 6416 0.554 11.700 -0.442 630VAL O1 6417 0.522 11.605 -0.534 630VAL O2 6418 0.534 11.834 -0.454 631<1> N2 1 2.686 2.399 2.151 631<1> C20 2 2.613 2.375 2.230 631<1> C14

[gmx-users] Re:RE:Crash error

Dear Justin, Thank you, that's the first help I have had. In any case, I will look at the .mdp file , as I was using a test structure I already ran through an MD. I had gone from 4.0.7 to 4.5.1 to 4.5.3, the first two ran MD's. Now I am rolling back too 4.0.7, but have not recieved complaint