Re: [gmx-users] Inconsistent Shifts

Dear Dallas, Yes, the system has periodic molecules (periodic-molecules = yes) and the version of gromacs is 5.1.2. So, I should use for calculating the properties of the system by gromacs 2016 and newer ones? Respectfully, Iman On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi

Re: [gmx-users] How to obtain TIP4P/ε water model topology file

Hi Mark, Thanks a lot for the suggestion. Just need a little more help. As per your suggestion I should edit the TIP3P topology. But the the forcefield (CHARMM36) has TIP4P.itp. Is there any advantage to edit TIP3P.itp instead of TIP4P.itp. Also I don't know what to edit. According to the

Re: [gmx-users] How to obtain TIP4P/ε water model topology file

Hi, Make a copy of your force field folder and edit the tip3p.itp file to suit. Even if someone had done this for you, you'd still want to be able to verify that this was the only change. Mark On Wed, Feb 21, 2018, 06:18 Tushar Ranjan Moharana < tusharranjanmohar...@gmail.com> wrote: > Hi

Re: [gmx-users] Electric Field

Thank you I'm trying to update it for external magnetic filed applications On Sun, Feb 18, 2018 at 12:57 PM, Mark Abraham wrote: > Hi, > > Suggestion, get the git version of gromacs and use > > git grep -i -G"electric field" > > src/gromacs/applied-forces > > Mark > >

Re: [gmx-users] How to obtain TIP4P/ε water model topology file

Hi Henriques, Thanks a lot for the suggestion. Actually it was TIP4P/(epsilon) which get modified to TIP4P/?. I regret for the same. I completely agree with your suggestion. Actually in an article (A fully atomistic computer simulation study of cold denaturation of a β-hairpin) authors have shown

Re: [gmx-users] Calculate RDF within a certain distance from atom

I have the RDF between Calpha-Ow, and it is showing a slight hump/peak around 0.47nm. So, i am further interested in studying how water molecules are oriented towards it closely...what is happening around within 0.7nm distance of Calpha w.r.t Ow... Any suggestions...?? Thank you. ‌

Re: [gmx-users] PROBLEM IN COORDINATES

On 2/20/18 9:50 PM, neelam wafa wrote: Dear gmx users I am still stuck at this point. error obtained is this Fatal error: number of coordinates in coordinate file (solv.gro, 32803) does not match topology (topol.top, 32818) There is a difference of 15. I think its not

Re: [gmx-users] PROBLEM IN COORDINATES

Dear gmx users I am still stuck at this point. error obtained is this Fatal error: number of coordinates in coordinate file (solv.gro, 32803) does not match topology (topol.top, 32818) There is a difference of 15. I think its not considering the ligand as 15 is i think for ligand.

Re: [gmx-users] About rdf in membranes

On 2/20/18 7:42 PM, Poncho Arvayo Zatarain wrote: The -xy is after or before the .ndx. I have this command gmx rdf -f file.xtc -s file.tpr -n file.ndx -xy -o file.xvg It doesn't matter. It's a boolean flag so it can appear anywhere in the command line that doesn't disrupt any other

Re: [gmx-users] About rdf in membranes

The -xy is after or before the .ndx. I have this command gmx rdf -f file.xtc -s file.tpr -n file.ndx -xy -o file.xvg De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se en nombre de Justin Lemkul

Re: [gmx-users] About rdf in membranes

On 2/20/18 7:03 PM, Poncho Arvayo Zatarain wrote: Hello Gromacs Users: I want to calculate rdf in membranes. I read i need something like .xy and i´m a little confussed. The command will be: gmx rdf -f file.xtc -s file.tpr -n file.ndx -xy -o file.xvg= What point is confusing? -Justin --

Re: [gmx-users] NVT NPT restrains

On 2/20/18 4:47 PM, Ahmed Mashaly wrote: Hi Justin I see the point of restraining heavy atoms in NPT.The problem is that; no posre  are included in the top file generated by Acpype, any suggestion to overcome that? Kind Regards,Ahmed Write in the directive yourself or generate it with

[gmx-users] About rdf in membranes

Hello Gromacs Users: I want to calculate rdf in membranes. I read i need something like .xy and i´m a little confussed. The command will be: gmx rdf -f file.xtc -s file.tpr -n file.ndx -xy -o file.xvg= Thanks for your help -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Inconsistent Shifts

What version of GROMACS are you using? Do you have periodic molecules in the system? i.e. periodic-molecules = yes in mdp file? Known bug, that has been recently fixed. https://redmine.gromacs.org/issues/2275 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute

Re: [gmx-users] NVT NPT restrains

Hi Justin I see the point of restraining heavy atoms in NPT.The problem is that; no posre  are included in the top file generated by Acpype, any suggestion to overcome that? Kind Regards,Ahmed From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Tuesday, February 20,

Re: [gmx-users] users list archive

On 2/20/18 1:58 PM, Lovas, Sandor wrote: For the past several days I am unable to reach/search the users list archive. I get the following error message when I try to load it: "Forbidden You don't have permission to access /pipermail/gromacs.org_gmx-users/ on this server. Apache/2.2.15 (Red

[gmx-users] users list archive

For the past several days I am unable to reach/search the users list archive. I get the following error message whrn I try to load it: "Forbidden You don't have permission to access /pipermail/gromacs.org_gmx-users/ on this server. Apache/2.2.15 (Red Hat) Server at mailman-1.sys.kth.se Port 443"

[gmx-users] users list archive

For the past several days I am unable to reach/search the users list archive. I get the following error message when I try to load it: "Forbidden You don't have permission to access /pipermail/gromacs.org_gmx-users/ on this server. Apache/2.2.15 (Red Hat) Server at mailman-1.sys.kth.se Port 443"

Re: [gmx-users] NVT NPT restrains

On 2/20/18 1:47 PM, Ahmed Mashaly wrote: Hi About the restrains, I see that it is necessary for NVT and NPT. For the .top and .gro produced by Acpype, https://drive.google.com/open?id=1K5IqAWb1_jXUfUPDjDtkOX2l8GuzbprM I don't have porse.itp nor anything related to restrain in the .top file,

Re: [gmx-users] energy minimization

On 2/20/18 12:52 PM, farial tavakoli wrote: blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear Justin Thank you for the reply You meant , to tweak the emtol doesn't have

[gmx-users] NVT NPT restrains

Hi About the restrains, I see that it is necessary for NVT and NPT. For the .top and .gro produced by Acpype, https://drive.google.com/open?id=1K5IqAWb1_jXUfUPDjDtkOX2l8GuzbprM I don't have porse.itp nor anything related to restrain in the .top file, only for water #ifdef FLEXIBLE [ bonds ] ;

Re: [gmx-users] energy minimization

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear Justin Thank you for the reply You meant , to tweak the emtol doesn't have noticable affects on the conformational

Re: [gmx-users] simulation time vs side chain flexibility

Thank you Justin. Ming On Tue, Feb 20, 2018 at 12:27 PM, Justin Lemkul wrote: > > > On 2/20/18 12:16 PM, MD wrote: > >> Thanks J. I agree. I should have added that the RMSD plateaued. And I am >> > > Don't let RMSD lull you into a false sense of security. If your side chain >

Re: [gmx-users] 2018 performance question

Hi Michael, What you observe is most likely due to v2018 by default shifting the PME work to the GPU which will often mean fewer CPU cores are needed and runs become more GPU-bound leaving the CPU without work for part of the runtime. This should be easily seen by comparing the log files.

Re: [gmx-users] energy minimization

On 2/20/18 4:52 AM, farial tavakoli wrote: Dear GMX users I used CHARMM36 all atom force field to generate .top and .gro files for my complex composed of a receptor protein and a ligand with 2 phosphotyrosine residues, then ran a md simulation on it and then used g_mmpbsa to calculate the

Re: [gmx-users] Energygrps

On 2/20/18 5:49 AM, Ahmed Mashaly wrote: Hi What is the default engerygrps to be written if I don't specify them in the mdp file? The default behavior is to not decompose the energy in any fashion, and just report it for the whole system. And if I have more than one ligand and want to

Re: [gmx-users] simulation time vs side chain flexibility

To be honest, I don't see how an increased side chain flexibility is proof that the protein is more flexible. They're not necessarily correlated. Protein flexibility involves larger movements concerning the protein backbone. These would probably be better captured by the RMSF, radius or gyration,

Re: [gmx-users] Calculate RDF within a certain distance from atom

On 2/20/18 11:53 AM, Dilip H N wrote: Hello, How to get RDF within a certain distance..?? Say for eg., i have glycine amino-acid and i want the RDF of Oxygen water atoms within 0.7nm of C-alpha (Calpha-Ow). how can i get it from in-house gmx rdf command...?? What do you hope to achieve

Re: [gmx-users] simulation time vs side chain flexibility

On 2/20/18 12:16 PM, MD wrote: Thanks J. I agree. I should have added that the RMSD plateaued. And I am Don't let RMSD lull you into a false sense of security. If your side chain gets "stuck" in one conformation, its RMSD will be low, but it tells you nothing about its flexibility because

Re: [gmx-users] simulation time vs side chain flexibility

Thanks J. I agree. I should have added that the RMSD plateaued. And I am more looking at side chain flexibility instead of secondary structure changes. Ming On Tue, Feb 20, 2018 at 12:09 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > This is not strictly a gromacs related question,

Re: [gmx-users] simulation time vs side chain flexibility

This is not strictly a gromacs related question, but long answer short: it depends, but most likely not. You must be able to convince people that the property you're interested in is properly converged within the simulation time you're considering. Multiple, reversible events need to be clearly

[gmx-users] Calculate RDF within a certain distance from atom

Hello, How to get RDF within a certain distance..?? Say for eg., i have glycine amino-acid and i want the RDF of Oxygen water atoms within 0.7nm of C-alpha (Calpha-Ow). how can i get it from in-house gmx rdf command...?? Any suggestions are appreciated... Thank you. -- With Best Regards,

[gmx-users] simulation time vs side chain flexibility

Hi Gromacs folks, I am trying to tell if a mutation can cause some part of the protein becoming more flexible. I started with the apo protein. I did two simulations in parallel, with one wild type and one with a silico mutation. After a 10 ns simulation I was able to tell some region of the

Re: [gmx-users] How to obtain TIP4P/ε water model topology file

I'm not very familiar with the TIP4P/ε water model, but if my memory serves me correctly, isn't it meant for pure water simulations? I'm not sure it's a good idea to mix it up with a protein force field without proper testing. Also, CHARMM36 was parametrized to be used with the CHARMM-modified

Re: [gmx-users] Worse GROMACS performance with better specs?

On Fri, Jan 12, 2018 at 2:35 AM, Jason Loo Siau Ee wrote: > Dear Carsten, > > Look's like we're seeing the same thing here, but only when using gcc 4.5.3: > > Original performance (gcc 5.3.1, AVX512, no hwloc support): 49 ns/day > > With hwloc support: > gcc 4.5.3,

[gmx-users] multi-replica runs with GPUs [fork of Re: Gromacs 2018 and GPU PME ]

Hi Dan, On Fri, Feb 9, 2018 at 4:56 PM, Daniel Kozuch wrote: > Szilárd, > > If I may jump in on this conversation, Let's fork the thread so the topics stay clear and discoverable by others, please. I am having the reverse problem > (which I assume others may encounter

[gmx-users] How to obtain TIP4P/ε water model topology file

Hi All, I want to use TIP4P/ε water model with CHARMM36 force field. Can anyone let me know where can I get the corresponding .itp file. Thanks a lot. "A society with free knowledge is better than a society with free food" -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB --

Re: [gmx-users] For non-zero entries for table x, the forces deviate from minus the numerical derivative of the potential

Hi, The simplest explanation is that the check is missing that factor, but we don't yet know that you have tested that the computed forces agree with your intention in the construction of the table. The computed energies are not an adequate test. To do that, you need to write the forces using an

Re: [gmx-users] For non-zero entries for table x, the forces deviate from minus the numerical derivative of the potential

Dear Mark, Thanks for your reaction! I have put the dihedral in a test system, where I freeze the positions of the atoms and calculate the energy of the system with the Tab.-Dih. option in gmx energy. The only dihedral in the system is the one from my own table, and the values are in pretty good

[gmx-users] Energygrps

Hi What is the default engerygrps to be written if I don't specify them in the mdp file? And if I have more than one ligand and want to calculate the energy between them and the protein, and also between one part of the protein (loop) and the rest of the protein I should make an index

Re: [gmx-users] For non-zero entries for table x, the forces deviate from minus the numerical derivative of the potential

Hi, It looks like somebody is missing a factor of 2; either you, or the check in the table code, or maybe also in the evaluation kernel. I suggest you set up a three-particle system, and make some coordinate files with those particles at carefully chosen angles and see what energy and force is

[gmx-users] energy minimization

Dear GMX users I used CHARMM36 all atom force field to generate .top and .gro files for my complex composed of a receptor protein and a ligand with 2 phosphotyrosine residues, then ran a md simulation on it and then used g_mmpbsa to calculate the binding free energy by pdies ( 2 and 4) but got

[gmx-users] For non-zero entries for table x, the forces deviate from minus the numerical derivative of the potential

Dear Gromacs users, I am currently trying to implement a user-defined dihedral into a coarse grained model (in version 5.1.4), but I get the following error: 'For the 35988 non-zero entries for table 0 in tables/table_d4.xvg the forces deviate on average 196% from minus the numerical derivative

Re: [gmx-users] Graphene simulation, regarding

Dear Alex Thank you On Tue, 20 Feb 2018 at 1:59 PM, Alex wrote: > This requires custom work, if you are determined to use Gromacs. > > If you actually read Andrea's full tutorial > (http://chembytes.wikidot.com/grocnt), it fully describes the basic > concept, so then it is

Re: [gmx-users] Graphene simulation, regarding

This requires custom work, if you are determined to use Gromacs. If you actually read Andrea's full tutorial (http://chembytes.wikidot.com/grocnt), it fully describes the basic concept, so then it is fairly clear how to proceed preparing files for x2top and then using it. For reduced GO you