[gmx-users] Problem with running Gromacs v. 5

Dear Gromacs users, I had to use newer version of Gromacs, so I install Gromacs 5.1.2 package. During installation I got no error. But I have serious problem with using it!! Since I always used older version of Gromacs that was somehow user friendlier!! My problem is how can I run gromacs from an

[gmx-users] Introduction of mutation into a PDB file, how?

Dear Gromacs users, I would like to introduce mutation into a pdb file which is going to be used for md simulations. Kindly suggest me the software otherthan SPDV. thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

Just to follow up on this, upgrading cmake from 2.8.8 (to 3.13 in this case) solved the problem. Adam From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Irina Kosheleva

Re: [gmx-users] Introduction of mutation into a PDB file, how?

Hi Seera, others options are UCSF chimera, VMD, and pymol Sent from Outlook Mobile On Tue, Feb 16, 2016 at 1:11 AM -0800, "Seera Suryanarayana" wrote: Dear Gromacs users, I would like to introduce mutation into a pdb file which is going to be used for md

Re: [gmx-users] calculate *all* carbon atom distances over time?

Hi Justin, Sorry to be a pain (and for probably asking a silly question...) but could you maybe elaborate on how the shell script you mentioned yesterday would loop over all combinations of interest? I'm not asking you to tell me how to write the script - just a bit how the idea would work, as

[gmx-users] Question about GROMACS

Dear All I have a quick question about GROMACS. Is there any chance to exert different types of loading such as torsional or bending or linear tension loading on simulation box in GROMACS ? Best wishes Ali khourshaei shargh (khourshaeisha...@mech.sharif.edu) Department of Mechanical

[gmx-users] Gromacs issue

Dear All I have a quick question about GROMACS. Is there any chance to exert different types of loading such as torsional or bending or linear tension loading on simulation box in GROMACS ? Best wishes Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir) Department of Mechanical

[gmx-users] Gromacs issue

Dear All I have a quick question about GROMACS. Is there any chance to exert different types of loading such as torsional or bending or linear tension loading on simulation box in GROMACS ? Best wishes Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir) Department of Mechanical Engineering

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 76

So, are there any other Amber force fields more suitable and more tested for GROMACS? 15.02.2016 21:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: Message: 1 Date: Mon, 15 Feb 2016 13:15:02 + From: Mark Abraham

Re: [gmx-users] GMX_USE_RTD SCP=OFF CMAKE option

Dear Mehreen, The error message is pretty instructive. Your gromacs installation was compiled for different hardware and you need to rebuild it as per the error message. Kind regards, Erik > On 16 Feb 2016, at 05:48, Mehreen Jan wrote: > > > > >> error: >> the

Re: [gmx-users] Not sure how to include dihedral angle params of ATP into force field

Hi, I have an itp for ATP that I made a while ago which has these parameters included. I can send it off list if you like? Cheers Tom From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 76

Hi, The ports of all the AMBER force fields were all tested to reproduce AMBER when when they were added to GROMACS. Many of our regressiontests use those force fields, so there is reason to expect that they all continue to work. The Verlet scheme is tested to implement what the documentation

Re: [gmx-users] Question about GROMACS

Hi, Yes, the deform .mdp option is intended to do these kinds of things, but I don't think there is more documentation than you can see here http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html#non-equilibrium-md, so look for a publication that reports using it. Mark On

Re: [gmx-users] Problem with running Gromacs v. 5

You might need to export the path in your ".bashrc" file In your case something like: export PATH=/source/gromacs-5.1.2/build:$PATH or even export PATH=/source/gromacs-5.1.2:$PATH And then refresh your .bashrc by logging out and logging in one time. Then you can use it where ever you are.

Re: [gmx-users] Problem with running Gromacs v. 5

Hi, On Tue, Feb 16, 2016 at 9:55 AM Mehrnoosh Hazrati < mehrnoosh.hazr...@modares.ac.ir> wrote: > Dear Gromacs users, > > I had to use newer version of Gromacs, so I install Gromacs 5.1.2 package. > During installation I got no error. But I have serious problem with using > it!! Since I always

[gmx-users] MPI and OpenMP threads

Dear Gromacs user, Gromacs works fine for me with the below first group of parallel environment and threads but it crashed with the second group complaining that: libgomp: Thread creation failed: Resource temporarily unavailable Thread creation failed: Resource temporarily unavailable Works

[gmx-users] error running grompp for ions.mdp input

hello I'm new to gromacs I'm simulating a protein in a mixed solvent (water/organic solvent) *first I added my organic solvent molecule (Methanol) using gmx insert-molecules command *then I solvate it in water using gmx solvate command but I went to adding atom using gmx grompp command

Re: [gmx-users] error running grompp for ions.mdp input

At the end of your topology file, make sure you have the correct number of molecules of each type (typically the end of the .top file will look something like: [ molecules ] Protein1;Number of proteins SOL59990 ;Number of waters Na 2 ; Number of Na ions Cl

Re: [gmx-users] MPI and OpenMP threads

Thanks for your response. I hope you mean with "what has been used in parallel environment" this: --- hard resource_list: h_rt=259000,h_vmem=6500M,h_stack=256M env_list: PSM_RANKS_PER_CONTEXT=4 parallel environment:

[gmx-users] Roadmap for new features

Dear all, Is there a place where the planned/hoped new features of Gromacs are listed? I am wondering if there is a chance that EVB, HREX (without the need to use plumed) or new QM/MM interface will be available at some point. I know that the developers are busy, but I am wondering what is in

[gmx-users] gmx chi output clarification

good afternoon, I'm trying to study the values of the omega dihedral (peptide bond) for a specific Proline in my protein. This Proline is known to exists in both cis and trans conformation(cis while binding). In the pdb I used as starting point for the simulation (2bhl.pdb) the Proline (172) is

Re: [gmx-users] MPI and OpenMP threads

On Tue, Feb 16, 2016 at 2:50 PM, Alexander Alexander wrote: > Thanks for your response. > > I hope you mean with "what has been used in parallel environment" this: > > --- > hard resource_list:

Re: [gmx-users] Roadmap for new features

Hi, On Tue, Feb 16, 2016 at 4:07 PM Nicolas Cheron < nicolas.cheron.bou...@gmail.com> wrote: > Dear all, > > Is there a place where the planned/hoped new features of Gromacs are > listed? Kind of. Many times people do some preliminary discussion on Redmine, and there's a large amount of stuff

[gmx-users] crosslinking polypeptide chains

Hi all, When executing pdb2gmx I am getting a fatal error due to dangling bonds. I know that it will be down to how I¹ve organised the .pdb file, I¹m just lacking in the experience with TERs, -chainsep and -merge to solve this. I would appreciate hints/tips/outright-solutions. My protein is very

Re: [gmx-users] gmx chi output clarification

On 2/16/16 10:16 AM, Francesco Carbone wrote: good afternoon, I'm trying to study the values of the omega dihedral (peptide bond) for a specific Proline in my protein. This Proline is known to exists in both cis and trans conformation(cis while binding). In the pdb I used as starting point

Re: [gmx-users] error running grompp for ions.mdp input

On 2/16/16 10:04 AM, Ghada Mhmd wrote: I'm still getting the same error but with different numbers even though I calculated the number of molecules of each [Moleculetype] in the .gro file and changed the number accordingly Then whatever you calculated was incorrect. A mismatch here is a

Re: [gmx-users] crosslinking polypeptide chains

Hi, Please start new topics in new emails, rather than confusing the web archives with replies to digests :-) On Tue, Feb 16, 2016 at 5:00 PM Nash, Anthony wrote: > Hi all, > > When executing pdb2gmx I am getting a fatal error due to dangling bonds. I > know that it will be

Re: [gmx-users] crosslinking polypeptide chains

On 2/16/16 10:59 AM, Nash, Anthony wrote: Hi all, When executing pdb2gmx I am getting a fatal error due to dangling bonds. I know that it will be down to how I¹ve organised the .pdb file, I¹m just lacking in the experience with TERs, -chainsep and -merge to solve this. I would appreciate

Re: [gmx-users] crosslinking polypeptide chains

Thank Justin and Mark, Apologies for not stripping out earlier content from my lazy “Reply” email. It was a slight of hand. It had crossed my mind to simply make two separate residues as you both suggested. Although I was trying to make most of this interchangeable with the Amber suite (this is

Re: [gmx-users] crosslinking polypeptide chains

On 2/16/16 11:22 AM, Nash, Anthony wrote: > Thank Justin and Mark, > > Apologies for not stripping out earlier content from my lazy “Reply” > email. It was a slight of hand. > > It had crossed my mind to simply make two separate residues as you both > suggested. Although I was trying to make

Re: [gmx-users] crosslinking polypeptide chains

Hi, What Justin said, plus IIRC you'll have two complete hydrogenated chains before specbond acts, so the two modified .rtp entries will want to have temporary hydrogen atoms that may as well neutralize their respective parts. specbond then strips them away, and you arrange for the result to have

[gmx-users] Problem with running Gromacs v. 5

> Different is necessarily unfriendly ;-) Yes!! :P >Don't try to install into your build tree. 5.1.2 should refuse to do so, >anyway. >That worked because by default the symlinks were made from a location that >was often in people's PATH variable. That's still true if you install into

[gmx-users] Density as a function of time

Hello Gromacs Users, I want to find the number of ions in a specific part (say left half) of the cell as a function of time. gmx density gives me a time average value across the box (cell), and I know that I can manually find the density for small time steps(0-1,1-2 ns...) and plot the values

Re: [gmx-users] Density as a function of time

On 2/16/16 12:22 PM, Ashutosh Akshay Shah wrote: Hello Gromacs Users, I want to find the number of ions in a specific part (say left half) of the cell as a function of time. gmx density gives me a time average value across the box (cell), and I know that I can manually find the density for

Re: [gmx-users] gmx chi output clarification

Thank you Justin, I selected the atoms (CA-C-N-CA) for the dihedral I want and check with "gmx angle" (gmx angle -f -n ciao.ndx -type dihedral) If I use the trajectory (-f file.xtc and ndx from a gro file) I have a nice distribution around 0° (avrg -3°) , while if I use the original pdb (-f

Re: [gmx-users] gmx chi output clarification

On 2/16/16 12:26 PM, Francesco Carbone wrote: Thank you Justin, I selected the atoms (CA-C-N-CA) for the dihedral I want and check with "gmx angle" (gmx angle -f -n ciao.ndx -type dihedral) If I use the trajectory (-f file.xtc and ndx from a gro file) I have a nice distribution around 0°

Re: [gmx-users] gmx chi output clarification

Thank you again for the quick response, I read that, but I'm calculating the omega angle which shouldn't be affected that how phi and psi are calculated. Furthermore, if I'm wrong, -1° it's not simply "usually small" different than 173°. Regards, Francesco On 16 February 2016 at 17:30,

Re: [gmx-users] gmx chi output clarification

On 2/16/16 12:40 PM, Francesco Carbone wrote: Thank you again for the quick response, I read that, but I'm calculating the omega angle which shouldn't be affected that how phi and psi are calculated. http://skryb.info/m/gmx-us...@gromacs.org/438c0b56.4020...@xray.bmc.uu.se Looks like

[gmx-users] NPT equilibration with small cell

Hello, I was wondering if there is any reason why one should expect a constant pressure simulation not to work for a small cell. I am running a very small cell (1.2 nm^3) simulation because I need it as input for ab initio MD. I am trying to simulate NPT at 1 atm and it seems like my cell, a

Re: [gmx-users] NPT equilibration with small cell

Hi, The cut-offs are not free parameters. The quality of the model physics depends on them (details are complex). Thus there is a minimum cell size that is workable with typical force fields. Mark On Tue, 16 Feb 2016 19:02 Miguel Caro wrote: > Hello, > > I was wondering

[gmx-users] Using make_ndx to combine many residues into 1 group

Dear Users, I have used make_ndx to combine several residues into a group before like " r 120 | r 150 | r 160 "... However now I need to combine residues from r 1 to r 166 ( all of them ) to create a group. Is there any short cut to this using make_ndx or do I need to write a python or shell

Re: [gmx-users] Using make_ndx to combine many residues into 1 group

On 2/16/16 1:57 PM, Agnivo Gosai wrote: Dear Users, I have used make_ndx to combine several residues into a group before like " r 120 | r 150 | r 160 "... However now I need to combine residues from r 1 to r 166 ( all of them ) to create a group. Is there any short cut to this using make_ndx

Re: [gmx-users] Density as a function of time

Thanks a ton Justin :) On Tue, Feb 16, 2016 at 12:23 PM, Justin Lemkul wrote: > > > On 2/16/16 12:22 PM, Ashutosh Akshay Shah wrote: > >> Hello Gromacs Users, >> >> I want to find the number of ions in a specific part (say left half) of >> the >> cell as a function of time. >>

Re: [gmx-users] NPT equilibration with small cell

Dear Mark, Thanks for your answer. I will try to learn more about how the cutoffs affect the simulation results. Is there any reading besides the manual that you could recommend on this topic? I would particularly appreciate anything on how to handle small cell simulations. Thanks again,

[gmx-users] [CfP] 5th IEEE Track on Collaborative Modeling and Simulation (Comets 2016) **** Submission Deadline Extended ****

*** Submission Deadline Extended ** (Please accept our apologies if you receive multiple copies of this message) # IEEE WETICE 2016 5th IEEE Track on Collaborative Modeling

Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Hello Mark. Your suggestions let me make and make install without errors gromacs-5.1.1. For libxml2: ./configure --prefix=/home/ikosh/programs/autotools-bin --without-python --without-zlib --without-lzma cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r

Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Hi, That commit's based off a development version of GROMACS, which naturally isn't as reliable as the released versions (or supported). I don't know why this wasn't working properly then, but probably cmake -DGMX_USE_TNG=off is enough to hack off the attempt to link zlib. Mark On Wed, Feb 17,

Re: [gmx-users] NPT equilibration with small cell

On 2/16/16 5:19 PM, Caro Miguel wrote: Dear Mark, Thanks for your answer. I will try to learn more about how the cutoffs affect the simulation results. Is there any reading besides the manual that you could recommend on this topic? I would particularly appreciate anything on how to handle

Re: [gmx-users] NPT equilibration with small cell

Dear Justin, Thanks for your very helpful answer. Miguel On 2016-02-17 02:32, Justin Lemkul wrote: On 2/16/16 5:19 PM, Caro Miguel wrote: Dear Mark, Thanks for your answer. I will try to learn more about how the cutoffs affect the simulation results. Is there any reading besides the