Re: [gmx-users] Error in Ligand position restraints

Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I successfully performed till perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat After this when I started performing en

[gmx-users] atoms are not part of any of the T-Coupling groups

Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created an index file that includes that atom, then created its posre.itp file and finally included following lines at the end of topol_Protein_cha

[gmx-users] Suggestions for Gromacs Perfomance

​Dear gmx users, I ​ have been performing some benchmarks as given taken from following URL, ​ ​​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ http://www.gromacs.org/GPU_acceleration ​​ ​The expected performance values is taken from the graph ​s​ . ​This cluster has a two nodes, of which one has two

Re: [gmx-users] Error in system_inflate.gro coordinates does not match

hello every one i am working on complex with popc membrane i got error in Deuterium Order Parameters group 1 does not have same number of elements as grp 1 i used the command make_ndx -f md_0_1.tpr -o sn1.ndx 0 System : 38483 atoms 1 Protein : 3873 atoms 2 Protein-H

Re: [gmx-users] Error in system_inflate.gro coordinates does not match

hello everyone i have been resolved the problem (del 0-23) all the elements but in output i got lots of warning WARNING: distance between atoms 9299 and 9301 > 0.3 nm (0.444934). Index file might be corrupt. WARNING: distance between atoms 9351 and 9353 > 0.3 nm (1.707690). Index file might be corr

[gmx-users] Pressures after NPT

dear gromacs users, I did an NPT equilibration of 100ps with a reference pressure of 1bar. After the equilibration, my average pressure was 1.2 bar. But when I started my production run (with a reference pressure of 1 bar) my pressure was rising (and falling) again. for the first 50 ps, the average

[gmx-users] User-PME

Hello gromacs users, I have a question about the mdp option User-PME. I am right in saying that if I choose a potential for the electrostatics, f(r) in my user tables, it is just for the real space part of the Ewald sum and then User-PME calculates the reciprocal and self-correction terms? Or

Re: [gmx-users] Simulation of Glass Surfaces?

Thank you for the information that does sound like it would do what I'm looking for, but could you possibly elaborate on how to set that up? I don't see either of those terms in the manual, either under the run parameters section about walls or otherwise. Thanks, AJ On Tue, Aug 5, 2014 at 2:53 P

Re: [gmx-users] Simulation of Glass Surfaces?

On 8/6/14, 8:01 AM, AJ Lanphere wrote: Thank you for the information that does sound like it would do what I'm looking for, but could you possibly elaborate on how to set that up? I don't see either of those terms in the manual, either under the run parameters section about walls or otherwise.

Re: [gmx-users] Protein simulation including ligand with Fe(III)

Hello again, Since I could not find any reliable parameters for the Fe-O for the GROMOS 96 forcefield I decided to modify it to use the parameters for its Fe-N in its HEME group. While reading through the gromos54a7 files i saw that it has parameters for the Fe-O bond so I thought that it might be

Re: [gmx-users] Pressures after NPT

On 8/6/14, 4:54 AM, ibrahim khalil wrote: dear gromacs users, I did an NPT equilibration of 100ps with a reference pressure of 1bar. After the equilibration, my average pressure was 1.2 bar. But when I started my production run (with a reference pressure of 1 bar) my pressure was rising (and fa

Re: [gmx-users] Simulation of Glass Surfaces?

I suppose I should have mentioned I'm using Gromacs 4.6.5. That section of the manual covers angular restraints, is that where I should be reading? Sorry for asking potentially inane questions, I'm not very experienced with this sort of thing. On Wed, Aug 6, 2014 at 10:18 AM, Justin Lemkul wrote

Re: [gmx-users] Simulation of Glass Surfaces?

On 8/6/14, 8:28 AM, AJ Lanphere wrote: I suppose I should have mentioned I'm using Gromacs 4.6.5. That section of the manual covers angular restraints, is that where I should be reading? Sorry for asking potentially inane questions, I'm not very experienced with this sort of thing. You need

Re: [gmx-users] Error in Ligand position restraints

On 8/6/14, 3:03 AM, neha bharti wrote: Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I successfully performed till perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.

Re: [gmx-users] atoms are not part of any of the T-Coupling groups

On 8/6/14, 3:46 AM, Nidhi Katyal wrote: Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created an index file that includes that atom, then created its posre.itp file and finally included fol

Re: [gmx-users] Protein simulation including ligand with Fe(III)

On 8/6/14, 8:19 AM, Nikolaos Michelarakis wrote: Hello again, Since I could not find any reliable parameters for the Fe-O for the GROMOS 96 forcefield I decided to modify it to use the parameters for its Fe-N in its HEME group. While reading through the gromos54a7 files i saw that it has param

Re: [gmx-users] Simulation of Glass Surfaces?

Alright, so that might not be an option for me. Can I configure the walls to accomplish a similar result in 4.6.5? On Wed, Aug 6, 2014 at 10:30 AM, Justin Lemkul wrote: > > > On 8/6/14, 8:28 AM, AJ Lanphere wrote: > >> I suppose I should have mentioned I'm using Gromacs 4.6.5. That section of >

Re: [gmx-users] User-PME

Hi, Haven't looked at the code, but the table maps to the real space part only, because it shares the implementation with the other kinds of user tables, for which reciprocal-space considerations do not apply. Mark On Wed, Aug 6, 2014 at 8:36 AM, O'Neill, David wrote: > Hello gromacs users, >

Re: [gmx-users] Why is there a NxN VdW [F] on a separate line?

On Tue, Aug 5, 2014 at 9:24 PM, Theodore Si wrote: > Please compare the file 8.log redir?resid=990FCE59E48164A4%212481&authkey=%21AI9ThbRY_ > 7ZgAg8&ithint=file%2clog> and 512.log redir?resid=990FCE59E48164A4%212482&authkey=% > 21APLkizO

Re: [gmx-users] Simulation of Glass Surfaces?

On 8/6/14, 8:59 AM, AJ Lanphere wrote: Alright, so that might not be an option for me. Can I configure the walls to accomplish a similar result in 4.6.5? Not in the context of what you originally asked for. The walls have to be defined as a type of material type, therefore the elements of

Re: [gmx-users] Protein simulation including ligand with Fe(III)

Here are the links: https://drive.google.com/file/d/0BzqRbRx4Ynf0c28zYVhoY3JRenM/edit?usp=sharing for the pdb file. https://drive.google.com/file/d/0BzqRbRx4Ynf0TmNsckliYWtqQUU/edit?usp=sharing for the topology. Cheers! -- Gromacs Users mailing list * Please search the archive at http://www

Re: [gmx-users] Protein simulation including ligand with Fe(III)

On 8/6/14, 9:26 AM, Nikolaos Michelarakis wrote: Here are the links: https://drive.google.com/file/d/0BzqRbRx4Ynf0c28zYVhoY3JRenM/edit?usp=sharing for the pdb file. The line for FE is misformatted (all the columns are aligned incorrectly), so it is simply ignored. -Justin https://drive.

Re: [gmx-users] User-PME

Mark, Thankyou for your response. Knowing this makes my life much easier, although I will of course run a test system to check. Regards, David From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: 06 August 2014 16:1

Re: [gmx-users] Simulation of Glass Surfaces?

Alright. Thank you very much for your assistance. On Wed, Aug 6, 2014 at 11:16 AM, Justin Lemkul wrote: > > > On 8/6/14, 8:59 AM, AJ Lanphere wrote: > >> Alright, so that might not be an option for me. Can I configure the walls >> to accomplish a similar result in 4.6.5? >> >> > Not in the cont

Re: [gmx-users] New residue in FF does not bond to others.

Thank you Justin. It helped but in my *top file I have still the old connection and the new ones. Can I simply delete connection I do not want? 2014-08-06 2:32 GMT+01:00 Justin Lemkul : > > > On 8/5/14, 11:59 AM, Dawid das wrote: > >> Dear Gromacs experts, >> >> I have found out why my force fie

Re: [gmx-users] New residue in FF does not bond to others.

Cause now what happens is that grompp requires bonding parameters for atoms which are actually bonded and for which are not (angle and dihedral parameters), e.g. CH6-Ser69 and CH6-Phe65 is what I want but I do not want connection between Ser69-Phe65. Now grompp asks me about bonding paramters for a

Re: [gmx-users] Any way to use GROMACS 4.6.x and 5 together

Dear Tamas and Mark, Thank you for your help. Since I am using GROMACS 4.6.x and 5, the default binary names are different, i.e., g_xxx versus gmx xxx, compiling with different suffixes are not necessary. It seems Mark's idea is most fault-proof, though sourcing different .bashrc files one at a ti

Re: [gmx-users] New residue in FF does not bond to others.

On 8/6/14, 12:04 PM, Dawid das wrote: Cause now what happens is that grompp requires bonding parameters for atoms which are actually bonded and for which are not (angle and dihedral parameters), e.g. CH6-Ser69 and CH6-Phe65 is what I want but I do not want connection between Ser69-Phe65. Now gr

Re: [gmx-users] Protein simulation including ligand with Fe(III)

Thanks a lot. Didn't realize that this would affect the topology. I now get an error that Fe is not in the residuetype.dat file. Since Gromos96 has parameters for Fe, shouldn't it be in the file? Just wondering. Thanks again, Nicholas -- Gromacs Users mailing list * Please search the archive a

Re: [gmx-users] New residue in FF does not bond to others.

Yes CH6 is defined as a Protein. In fact pdb2gmx sees two chains. How to work it out then? 2014-08-06 19:45 GMT+01:00 Justin Lemkul : > > > On 8/6/14, 12:04 PM, Dawid das wrote: > >> Cause now what happens is that grompp requires bonding parameters for >> atoms >> which are actually bonded and f

Re: [gmx-users] Protein simulation including ligand with Fe(III)

On 8/6/14, 12:50 PM, Nikolaos Michelarakis wrote: Thanks a lot. Didn't realize that this would affect the topology. I now get an error that Fe is not in the residuetype.dat file. Since Gromos96 has parameters for Fe, shouldn't it be in the file? Just wondering. Only things defined as residu

Re: [gmx-users] New residue in FF does not bond to others.

On 8/6/14, 12:52 PM, Dawid das wrote: Yes CH6 is defined as a Protein. In fact pdb2gmx sees two chains. How to work it out then? You'll need to provide files and describe exactly what the problems are (lines in the topology, please) and what changes you have made since the last bundle of f

Re: [gmx-users] New residue in FF does not bond to others.

These are lines that cause trouble: ERROR 1 [file mCherry7.top, line 18183]: No default U-B types ERROR 2 [file mCherry7.top, line 18250]: No default U-B types ERROR 3 [file mCherry7.top, line 25379]: No default Proper Dih. types ERROR 4 [file mCherry7.top, line 25380]: No default Pr

[gmx-users] gmx 4.6.6: rvdw == rcoulomb for Verlet lists

Good afternoon! When using the Verlet lists cut-off scheme, grompp will throw an error if the values for both *rcoulomb* and *rvdw* are not the same. However, when performing md with *mdrun* and *-tunepme yes*, the coulomb cutoff will be adjusted along with the pme grid to improve performance.

Re: [gmx-users] pdb2gmx cannot generate the right residue and atom numbers

Thank you for your reply. I am just wondering is there anyway we can make pdb2gmx change the default digit number? I am doing a membrane protein, and I already have a ideal model as a pdb file. If I need to go over the solvate(or genbox in the 4.5.x version), by default waterbox setting the wate

Re: [gmx-users] New residue in FF does not bond to others.

On 8/6/14, 1:36 PM, Dawid das wrote: These are lines that cause trouble: ERROR 1 [file mCherry7.top, line 18183]: No default U-B types ERROR 2 [file mCherry7.top, line 18250]: No default U-B types ERROR 3 [file mCherry7.top, line 25379]: No default Proper Dih. types ERROR 4 [fil

Re: [gmx-users] gmx 4.6.6: rvdw == rcoulomb for Verlet lists

On 8/6/14, 3:56 PM, David Dotson wrote: Good afternoon! When using the Verlet lists cut-off scheme, grompp will throw an error if the values for both *rcoulomb* and *rvdw* are not the same. However, when performing md with *mdrun* and *-tunepme yes*, the coulomb cutoff will be adjusted along w

[gmx-users] ligand binding

hello I have used charmm27 force field to parametrize my protein(human serum albumin,584a.a) and swiss param to provide parameters to the ligand due to which coordinates of ligand is changed and active site of protein is also completely changed. Can anybody tell me that ligand coordinates should be

Re: [gmx-users] gmx 4.6.6: rvdw == rcoulomb for Verlet lists

Thanks for the clear reply Justin. If *rvdw* does not change, that is enough for me. Out of curiosity, what is the technical reason for the requirement "rcoulomb = rvdw", especially if rcoulomb is allowed to change during the simulation from tuning? David On 08/06/2014 06:28 PM, Justin Lemk

Re: [gmx-users] pdb2gmx cannot generate the right residue and atom numbers

Sure, but by writing your model in .pdb you have thrown away important information. If you can't write it in another format and won't re-solvate, then you might have to try strategies like converting it to .gro with editconf and fixing the numbering by hand/script. Mark On Wed, Aug 6, 2014 at 8:

Re: [gmx-users] User-PME

Good idea. If my idea is right, then you should be able to change the table and observe that the reciprocal space part does not change... I would certainly look at what the potential is for systems for two atoms at a range of distances. Mark On Wed, Aug 6, 2014 at 11:44 AM, O'Neill, David wrote

Re: [gmx-users] atoms are not part of any of the T-Coupling groups

gmxcheck of my index file gives: Contents of index file index.ndx -- Nr. Group #Entries FirstLast 0 System 2230 12230 1 Protein 2226 12226 2 Protein-H