[gmx-users] Umbrella Sampling - NPT

Dear Justin, I am wondering whether in NPT simulations before umbrella sampling in each window the option: continuation = yes should be set to continuation = no as you provided 1st option. Thank you, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/list

[gmx-users] cannot determine precision of trn file

Dear All, I was running my simulation for 30ns but at the last step i got following error: "Cannot close energy file;it might be corrupt, or maybe you are out of quota." It was found that there was some disk space problem but when the issue was resolved i restarted my run from the last step using

[gmx-users] Distance between selected atoms during simulation

Dear Gromacs Users! I want to perform measurements of the distances between backbone as well as side-chain atoms of the selected residues using gro and trajectory files. What Gromacs program should I use for such measurements? James -- gmx-users mailing listgmx-users@gromacs.org http://li

Re: [gmx-users] cannot determine precision of trn file

On 5/03/2012 8:48 PM, Nidhi Katyal wrote: Dear All, I was running my simulation for 30ns but at the last step i got following error: "Cannot close energy file;it might be corrupt, or maybe you are out of quota." It was found that there was some disk space problem but when the issue was resolv

Re: [gmx-users] Distance between selected atoms during simulation

On 5/03/2012 8:48 PM, James Starlight wrote: Dear Gromacs Users! I want to perform measurements of the distances between backbone as well as side-chain atoms of the selected residues using gro and trajectory files. What Gromacs program should I use for such measurements? Check out manual

[gmx-users] Simple LJ system

I have literally just started using gromacs and hopefully have a pretty straight forward question. Firstly I am interested in simulating a binary Lennard-jones system with arbitrary choices of parameters (i.e. I may choose the epsilon and sigma). If someone could summarise what ingredients I wo

Re: [gmx-users] Re: Gromacs-GPU benchmark test killed after exhausting the memory

Hi Efrat, It indeed looks like a memory leak. Could you please file a bug on redmine.gromacs.org? Cheers, -- Szilárd On Sun, Mar 4, 2012 at 12:21 PM, Efrat Exlrod wrote: > Hi Szilard, > > Thanks for your reply. > I used your script and I think it does look as a memory leak. Please look at >

[gmx-users] [ bondedtypes ]

Thanks for your help. :-)  I did not realize that table 5.5 corresponds to [ bondedtypes ] Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search befor

[gmx-users] a warning in grompp

dear all; I am trying to run grompp command and I encounter this: . WARNING 1 [file topol.top, line 54]: The bond in molecule-type DNA_chain_A between atoms 1 H5T and 2 O5' has an estimated oscillational period of 9.0e

[gmx-users] How to answer in this mailing list?

Hello I wrote an email to the mailing list with the subject [ bondedtypes ] and I got answers that helped me. I wanted to answer to this by a new email with same subject and the mailing list create a new question out of it. How do I answer in this mailing list to a topic? Thanks Greetings La

[gmx-users] g_msd segmentation fault

Dear All I have a system of 40 solute molecules in 480 crown ether solvent molecules. When I ran the msd analysis on the solvent molecules using the following comand. g_msd_login_d -f traj.trr -s topol.tpr -mol -o 1_12_400K_sol_msd.xvg I get a segmentation fault as follows Select a group: 4

Re: [gmx-users] a warning in grompp

Banafsheh Mehrazma wrote: dear all; I am trying to run grompp command and I encounter this: . WARNING 1 [file topol.top, line 54]: The bond in molecule-type DNA_chain_A between atoms 1 H5T and 2 O5' has an estima

Re: [gmx-users] How to answer in this mailing list?

On 5/03/2012 11:39 PM, Lara Bunte wrote: Hello I wrote an email to the mailing list with the subject [ bondedtypes ] and I got answers that helped me. I wanted to answer to this by a new email with same subject and the mailing list create a new question out of it. How do I answer in this mail

Re: [gmx-users] g_msd segmentation fault

On 5/03/2012 11:39 PM, Gavin Melaugh wrote: Dear All I have a system of 40 solute molecules in 480 crown ether solvent molecules. When I ran the msd analysis on the solvent molecules using the following comand. g_msd_login_d -f traj.trr -s topol.tpr -mol -o 1_12_400K_sol_msd.xvg I get a segme

Re: [gmx-users] How to answer in this mailing list?

Hi Thanks for answer. This is also a test if it work :-) Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)su

Re: [gmx-users] Simple LJ system

Jeff Armstrong wrote: I have literally just started using gromacs and hopefully have a pretty straight forward question. Firstly I am interested in simulating a binary Lennard-jones system with arbitrary choices of parameters (i.e. I may choose the epsilon and sigma). If someone could summari

Re: [gmx-users] Re: how modify the forcefield amino acid definitions for non-naturally occuring amino acids?

Kirill Bessonov wrote: Thank you Justin for your prompt reply, as usual :) With the last 2 lines of my previous post, I was referring on how to build *.itp files for completely new molecules (say lipids such as DMPC, DMPE or glutathione) that are not defined in the forcefield. I.e. how to d

Re: [gmx-users] Umbrella Sampling - NPT

Steven Neumann wrote: Dear Justin, I am wondering whether in NPT simulations before umbrella sampling in each window the option: continuation = yes should be set to continuation = no as you provided 1st option. The starting structures were the product of simulations that were previously

Re: [gmx-users] g_msd segmentation fault

On Mon, 2012-03-05 at 23:56 +1100, Mark Abraham wrote: > On 5/03/2012 11:39 PM, Gavin Melaugh wrote: > > Dear All > > > > I have a system of 40 solute molecules in 480 crown ether solvent molecules. > > When I ran the msd analysis on the solvent molecules using the following > > comand. > > > > g_

Re: [gmx-users] cannot determine precision of trn file

I think my restart was achieved successfully as my err file contained following lines: "reading checkpoint file state.cpt generated: Loaded with memory making 2D domain decomposition 4*2*1 starting mdrun 'protein in water' 1500 steps, 3.0ps(continuing from step 1500, 3.0ps)." Also

Re: [gmx-users] Re: Lennard-Jones Interactions in Gromacs

Please make sure to send replies to the list (gmx-users@gromacs.org) rather than my personal inbox. Lara Bunte wrote: Hi Thank you for helping me. I still don't get it. Out of the support of charmm force field I have a document with following parameters: ATOM NAMEATOM TYPE

[gmx-users] Imitation of the protein part

Hi Gmx Users, I am simulationg parts of the big protein so in this case imitating non charged terminals. For this purpose I use option: pdb2gmx -f Protein.pdb -ter Which option would be suitable and safe to imitate it: a) NH2 and COOH b) None Thank you! Steven -- gmx-users mailing listgmx-

Re: [gmx-users] Acpype Parameter Error?

Kyle, can you send and pdb file so I can reproduce your issue? Thanks, Alan On 24 February 2012 23:25, Kyle Greenway wrote: > > Hello, > > This email is directed mainly to Alan, who created Acpype. > > I've noticed that Acpype has assigned dihedral constants as 0.65084 for > many dihedrals of

[gmx-users] segmentation fault err

Dear gmx-users, I'm facing "segmentation fault error" while *mdrun*. When i checked my md.log file, after 440'th step the kinetic energy energy increases by tenfold and hence the temperature (temp - 6.80141e+01K to 2.21829e+02K). all other values, potential energy etc. are not changing much so

[gmx-users] folding of coordinates in trajectory files

Hi All I was wondering. I assume gromacs writes folded coordinates in the trajectory files. If so does it use rx(i) = rx(i) -boxl *nint(rx(i) / boxl) to fold the coordinates at each step? and where does it define the origin (0,0,0) Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.or

Re: [gmx-users] Imitation of the protein part

Specifying "none" for the termini, in conjunction with suitable capping groups to create uncharged peptide bonds at the termini (which have to be built on with external software), is the best approach to modeling such a system, in my opinion. -Justin Steven Neumann wrote: Hi Gmx Users, I

Re: [gmx-users] segmentation fault err

On 6/03/2012 2:58 AM, shilpa yadahalli wrote: Dear gmx-users, I'm facing "segmentation fault error" while *mdrun*. When i checked my md.log file, after 440'th step the kinetic energy energy increases by tenfold and hence the temperature (temp - 6.80141e+01K to 2.21829e+02K). all other values,

Re: [gmx-users] folding of coordinates in trajectory files

Hey Gavin, still can't get the binary system to run. if I give you the files I am using could you have a quick peak and see if I am doing anything obviously wrong? Jeff -- Jeff Armstrong Department of Chemistry, Imperial College, SW7 2AZ, London, United Kingdom -- gmx-users mailing list

Re: [gmx-users] folding of coordinates in trajectory files

On 6/03/2012 2:59 AM, Gavin Melaugh wrote: Hi All I was wondering. I assume gromacs writes folded coordinates in the trajectory files. If so does it use rx(i) = rx(i) -boxl *nint(rx(i) / boxl) to fold the coordinates at each step? and where does it define the origin (0,0,0) GROMACS suits it

Re: [gmx-users] cannot determine precision of trn file

On 6/03/2012 12:30 AM, Nidhi Katyal wrote: I think my restart was achieved successfully as my err file contained following lines: "reading checkpoint file state.cpt generated: Loaded with memory making 2D domain decomposition 4*2*1 starting mdrun 'protein in water' 1500 steps, 3.0ps(cont

[gmx-users] em.mdp file

Hello Is this em.mdp file correct for a simple MD simulation? integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 nstenergy = 10 Thanks for help Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://

RE: [gmx-users] em.mdp file

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Lara Bunte [lara.bu...@yahoo.de] Sent: Monday, March 05, 2012 5:24 PM To: gmx-users@gromacs.org Subject: [gmx-users] em.mdp file Hello Is this em.mdp file correct for a sim

Re: [gmx-users] em.mdp file

Lara Bunte wrote: Hello Is this em.mdp file correct for a simple MD simulation? integrator = steep nsteps = 200 nstlist = 10 You should set nstlist=1 for energy minimization (which is not, by definition, MD). -Justin rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off

Re: [gmx-users] em.mdp file

Justin A. Lemkul wrote: Lara Bunte wrote: Hello Is this em.mdp file correct for a simple MD simulation? integrator = steep nsteps = 200 nstlist = 10 You should set nstlist=1 for energy minimization (which is not, by definition, MD). Hit "send" too soon... You have also specified

[gmx-users] grompp error - bondedtypes

Hi I used the command grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr and get this errors: ERROR 1 [file flavin.rtp, line 1]:   Invalid directive bondedtypes ERROR 2 [file flavin.rtp, line 7]:   Not enough parameters I know where this error occurs from but I don't know what is fa

Re: [gmx-users] grompp error - bondedtypes

Lara Bunte wrote: Hi I used the command grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr and get this errors: ERROR 1 [file flavin.rtp, line 1]: Invalid directive bondedtypes ERROR 2 [file flavin.rtp, line 7]: Not enough parameters I know where this error occurs from but

Re: [gmx-users] grompp error - bondedtypes

Lara Bunte wrote: Yes it was included in forcefield.itp Only pdb2gmx uses .rtp files (see the manual). Thanks for your help Know I got the error No default Fourier Dih. types What should I do? You need a corresponding [dihedraltypes] for all dihedrals in the system. The error i

Re:Re: [gmx-users] grompp error - bondedtypes

"Justin A. Lemkul" wrote: Lara Bunte wrote: > Yes it was included in forcefield.itp > Only pdb2gmx uses .rtp files (see the manual). > Thanks for your help > > Know I got the error > > > No default Fourier Dih. types > > > What should I do? > You need a corresponding [dihedraltypes] for all

[gmx-users] a question related to MD by gromacs

Dear All,   I plan to do 1 ns MD for a protein with MW 50, 000 by gromacs. As for my gromacs was installed in the cygwin by a laptop, I cannot run it day and night, which means my 1 ns MD needs to have a lot of stops and restart.   Will you please remind me the gromacs command to reinstiate the g

Re: [gmx-users] a question related to MD by gromacs

Dialing Pretty wrote: Dear All, I plan to do 1 ns MD for a protein with MW 50, 000 by gromacs. As for my gromacs was installed in the cygwin by a laptop, I cannot run it day and night, which means my 1 ns MD needs to have a lot of stops and restart. Will you please remind me the gromacs c

[gmx-users] spatial distribution function

I am trying to calculate spatial distribution function (SDF) for ionic liquid.I want to see the distribution of anion around cation. I followed the steps given in gromacs manual.I created two groups each of single cation and all anions in the index file and did two steps trj