[gmx-users] table extension

Dear GMXs, I would like to clear something out, for myself: The table extension given in MDP file applies to "nonbond_params" & "pairs" interactions which are specified in the TOP file (and also electrostatics)? Is there an interaction which does not use the table extension (other then bonds, angle

[gmx-users] molecule ouside water box

Hi gmx users, I defined an octahedral box with this line: $grxdir/editconf -f 1AKEallH.gro -o 1AKEallHbox.gro -bt octahedron -d 0.6 and then I solvated my protein with SPC water model: $grxdir/genbox -cp 1AKEallHbox.gro -p 1AKEallH.top -o 1AKEallHsol.gro -cs I am now watching the trajectory o

Re: [gmx-users] molecule ouside water box

Stefano Meliga wrote: Hi gmx users, I defined an octahedral box with this line: $grxdir/editconf -f 1AKEallH.gro -o 1AKEallHbox.gro -bt octahedron -d 0.6 and then I solvated my protein with SPC water model: $grxdir/genbox -cp 1AKEallHbox.gro -p 1AKEallH.top -o 1AKEallHsol.gro -cs I am now

[gmx-users] Re: HEME-cysteine gromacs simulation (zimohmily)

Thanks both Mark and chris.ne...@utoronto.ca 's advises. Listening to these words of yours,is better than learning for ten years. Most people uses the AMBER force field to run HEME simulation,I should focus on suitable force field and associated correct parameters.thanks > 1. Re: HEME-cystei

Re: [gmx-users] table extension

Omer Markovitch wrote: Dear GMXs, I would like to clear something out, for myself: The table extension given in MDP file applies to "nonbond_params" & "pairs" interactions which are specified in the TOP file (and also electrostatics)? From 7.3.12, yes. These are the nonbonded interactions. Is

[gmx-users] Converting pdb to Amber (to use with ffamber99)

Hi all, I am looking for a simple way to convert amino acid and nucleic residues from the PDB standard to the AMBER Nomenclature (to use with ffamber99 in GROMACS). Your help is appreciated. Nehme. ___ gmx-users mailing listgmx-users@gromacs.

Re: [gmx-users] Converting pdb to Amber (to use with ffamber99)

Nehme El Hachem wrote: Hi all, I am looking for a simple way to convert amino acid and nucleic residues from the PDB standard to the AMBER Nomenclature (to use with ffamber99 in GROMACS). Your help is appreciated. Simple scripting (like Perl) or shell commands (vi, emacs editors or sed).

[gmx-users] Exploding poly-serine

Hi, I am trying to work my way through learning to use GROMACS 4.0.5 for doing MD simulations of short peptides in solution. My problem is that several peptides, most strikingly a Serine 10-mer, are exploding during the production run. I construct the serine polymer in extended form us

Re: [gmx-users] Exploding poly-serine

Warren Gallin wrote: Hi, I am trying to work my way through learning to use GROMACS 4.0.5 for doing MD simulations of short peptides in solution. My problem is that several peptides, most strikingly a Serine 10-mer, are exploding during the production run. I construct the ser

Re: [gmx-users] Exploding poly-serine

Warren Gallin wrote: Hi, I am trying to work my way through learning to use GROMACS 4.0.5 for doing MD simulations of short peptides in solution. My problem is that several peptides, most strikingly a Serine 10-mer, are exploding during the production run. I construct the serin

Re: [gmx-users] Exploding poly-serine

David, That is probably it, I had a 2-femtosecond step and no bond constraints. Obviously I need to read up on the pros and cons of the various restraint regimes. I guess that would be consistent with the sudden explosion after along period of stable running. Why poly-Ser would be m

Re: [gmx-users] LINCS

Hi Justin, I tried to run full MD after energy minimization in both vacuo and water... went good but I got this ERROR once I try to run full MD. Can you please help. = Step 0, time 0 (ps) LINCS WARNING relative constraint devia

Re: [gmx-users] LINCS

tekle...@ualberta.ca wrote: Hi Justin, I tried to run full MD after energy minimization in both vacuo and water... went good but I got this ERROR once I try to run full MD. Can you please help. There is something physically unrealistic about your model. That's the case whenever you

[gmx-users] Problem in Energy minimisation for a rigid body system

Hi, I want to do a rigid body simulation for a 7-site model system, where the center is occupied by a metal ion and the 6 octahedral sites are occupied by 6 dummy atoms. Initially I tried to simulate a 5-site square planar rigid body system, where the center is occupied by the metal atom and four

[gmx-users] is the D G sol of g_sas useless? why?

Hi gmxs, I'm trying to compute a aproximated D G of binding between two proteins using a termodynamic cycle, and the D Gsol calculated with g_sas (from 10 ns dynamics for every situation) But I had read here, that the value this way calculated is useless why? Waiting for answer - Felipe

Re: [gmx-users] is the D G sol of g_sas useless? why?

Felipe Villanelo wrote: Hi gmxs, I'm trying to compute a aproximated D G of binding between two proteins using a termodynamic cycle, and the D Gsol calculated with g_sas (from 10 ns dynamics for every situation) But I had read here, that the value this way calculated is useless why? If you

Re: [gmx-users] Exploding poly-serine

Warren Gallin wrote: David, That is probably it, I had a 2-femtosecond step and no bond constraints. Obviously I need to read up on the pros and cons of the various restraint regimes. I guess that would be consistent with the sudden explosion after along period of stable running.

[gmx-users] wierd behavior of mdrun

I made a .tpr file for my md run without any problems (using the bottom mdp file). My job submission script is also the same thing I used for other jobs which had no problems. But now when I submit this .tpr file, only an empty log file is generated! The qstat of the cluster shows that the job is r

Re: [gmx-users] Problem in Energy minimisation for a rigid body system

dbis...@ucalgary.ca wrote: Hi, I want to do a rigid body simulation for a 7-site model system, where the center is occupied by a metal ion and the 6 octahedral sites are occupied by 6 dummy atoms. Initially I tried to simulate a 5-site square planar rigid body system, where the center is occupie

Re: [gmx-users] wierd behavior of mdrun

Paymon Pirzadeh wrote: I made a .tpr file for my md run without any problems (using the bottom mdp file). My job submission script is also the same thing I used for other jobs which had no problems. But now when I submit this .tpr file, only an empty log file is generated! The qstat of the cluste

Re: [gmx-users] Problem in Energy minimisation for a rigid body system

Hi Mark, Initially I included all the sets of bonds (as you have mentioned). Then I get the warning message while doing grompp, which says number of constraints is more (18 as I've defined) than required (it shouldn't be more than 15). With all the sets of bonds defined also, energy minimization d

Re: [gmx-users] is the D G sol of g_sas useless? why?

Felipe Villanelo wrote: Hi gmxs, I'm trying to compute a aproximated D G of binding between two proteins using a termodynamic cycle, and the D Gsol calculated with g_sas (from 10 ns dynamics for every situation) But I had read here, that the value this way calculated is useless why? Firs

[gmx-users] Re: wierd behavior of mdrun

> I made a .tpr file for my md run without any problems (using the bottom > mdp file). My job submission script is also the same thing I used for > other jobs which had no problems. But now when I submit this .tpr file, > only an empty log file is generated! The qstat of the cluster shows that > th

Re: [gmx-users] Re: gmx-users Digest, Vol 64, Issue 17

Dear Gerrit, On the website below you state all basissets were available. I tried to use 6-311G* and got an error message stating 6-311G* wasn't available. Have you implemented in the meantime? Or is there any extra installation package required? I use gromacs-4.0.5 My question about Freq