[gmx-users] generating full atomic structure

Dear all, I got a pdb file including the C-alpha itoms of different residues only. Is there any software that can add the other atoms of the residues to the pdb file automatically? Thanks in advance, Ming -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Su

[gmx-users] A query

Dear All, *gcq#6: "It's So Lonely When You Don't Even Know Yourself" (Red Hot Chili Peppers)* Such messages pop up after running the gromacs commands on terminal. Do these messages have any meaning ? Have they anything to do with the programs we are running? -- *Let us all join hands to save o

Re: [gmx-users] A query

Nope! They are just for our amusement. Maybe only one has to do it: "Check your input!" David van der Spoel Cheers! Marcelo Depólo Em 13/04/2015 07:05, "Priya Das" escreveu: > Dear All, > > > *gcq#6: "It's So Lonely When You Don't Even Know Yourself" (Red Hot Chili > Peppers)* > Such messages p

Re: [gmx-users] A query

Hi Priya, Yes, this particular message means that you should also get to know yourself, because it is key to understand others, which is the most important step to not being lonely. This one may not be directly related to the program, but in terms of science, it sort of suggests that you should no

[gmx-users] how to modify the files in the force field fold of Gromacs

Dear all, I need to modify the .rtp file in charmm27.ff, but I can do nothing. How to change the access to those files? Thanks in advance, Ming -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't pos

Re: [gmx-users] Can NAMD simulation solve the problem of coordinate clash in a structural model?

Hi Yeping Sun, If the coordinates are garbled (what are serious coordinate clashes?), you'll have a hard time with either NAMD or Gromacs. Cheers, Tsjerk On Mon, Apr 13, 2015 at 6:05 AM, sunyeping wrote: > > Dear all, > > I modelled a structural model of a complex containing two large protein

Re: [gmx-users] how to modify the files in the force field fold of Gromacs

Hi Ming, Copy the whole folder to your working directory. Gromacs will give force field files in the working directory precedence. Cheers, Tsjerk On Mon, Apr 13, 2015 at 12:32 PM, Ming Tang wrote: > Dear all, > > I need to modify the .rtp file in charmm27.ff, but I can do nothing. How > to ch

Re: [gmx-users] A simple question

Hi Saeed, Attachments don't work with the mailing list. Could you copy a few lines of the pdb for us to look at and maybe upload the pdb you generated to dropbox or a similar site? Also pdb2gmx may not be the best route here. You may need to explicitly write your own topology file (tedious as

Re: [gmx-users] How to add a repulsive harmonic potential

On 4/12/15 10:40 PM, atsutoshi.ok...@takeda.com wrote: Thank you for your help. Actually, I want to predict the binding mode of ligand for protein/ligand complex during long time simulation, so I want to add only repulsive potential between ligands to avoid ligand aggregation, not fix these

Re: [gmx-users] In-Vacuo ligand only equilibration

On 4/13/15 12:38 AM, Iris Nira Smith wrote: Hello, I'm utilizing gromacs 4.6.3 to set up my md simulation to run a ligand-only invacuo (no water) system for 500 ps prior to running my protein-ligand complex to determine the stability of the ligand. I have successfully run an energy minimiza

Re: [gmx-users] A simple question

On 4/13/15 2:29 AM, saeed poorasad wrote: Hi . Dear Gromacs users . Today is the first day that i am working with GROMACS .I want to have a system with one C60 and about 1000 water molecules .I tried to use pdb2gmx on C60.pdb but I got fatal error , I think the problem is because of my PDB fi

Re: [gmx-users] How to add a repulsive harmonic potential

Hi, For distance restraints, there is also an mdp section in which you must choose values. Mark On 13/04/2015 4:42 am, wrote: > Thank you for your help. > Actually, I want to predict the binding mode of ligand for protein/ligand > complex during long time simulation, so I want to add only repul

Re: [gmx-users] A query

Hi, Yes, there are a few programs in computational chemistry that give such quotes randomly; GAUSSIAN comes to mind. There's an environment variable described in one of the manual appendices that will disable them, if you prefer. Mark On 13/04/2015 12:25 pm, "Tsjerk Wassenaar" wrote: > Hi Priya

[gmx-users] Effect of hardware threads mismatch on simulation

Dear gmx-users, When running a simulation of a protein in solution on my university’s cluster I get the two following notifications: Number of hardware threads detected (20) does not match the number reported by OpenMP (1). Consider setting the launch configuration manually! Non-default thread a

Re: [gmx-users] generating full atomic structure

if your file is missing only the hydrogens, openbabel can add them for you. If your file is missing heavier atoms, I don't know. Hope this helps Victor 2015-04-13 2:00 GMT-05:00 Ming Tang : > Dear all, > > I got a pdb file including the C-alpha itoms of different residues only. Is > there any

[gmx-users] refcoord-scaling without pressure coupling

Dear GMX users, If I set "refcoord-scaling = com" and also "pcoupl = no", will that "refcoord-scaling = com" do anything (like introducing additional numerical error in a NVE simulation) ? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Ma

Re: [gmx-users] refcoord-scaling without pressure coupling

On 4/13/15 9:44 AM, Johnny Lu wrote: Dear GMX users, If I set "refcoord-scaling = com" and also "pcoupl = no", will that "refcoord-scaling = com" do anything (like introducing additional numerical error in a NVE simulation) ? No. The option is only relevant with pressure coupling. -Justin

Re: [gmx-users] refcoord-scaling without pressure coupling

Thank you! Next time I don't have to swing the mouse to make the door open (even when swing the mouse does nothing). On Mon, Apr 13, 2015 at 9:46 AM, Justin Lemkul wrote: > > > On 4/13/15 9:44 AM, Johnny Lu wrote: > >> Dear GMX users, >> >> If I set "refcoord-scaling = com" and also "pcoupl = n

Re: [gmx-users] generating full atomic structure

Thanks. It contains alpha carbons only. Sent from my Huawei Mobile Victor Rosas Garcia wrote: if your file is missing only the hydrogens, openbabel can add them for you. If your file is missing heavier atoms, I don't know. Hope this helps Victor 2015-04-13 2:00 GMT-05:00 Ming Tang : > Dear

Re: [gmx-users] In-Vacuo ligand only equilibration (Iris Nira Smith)

Thank you Justin for your insight to your previous response. I made adjustments to my equilibration .mdp file (below) to run as NVT in vacuo. Can you review and advise on corrections? eqb-nvt-invacuo.mdp ;Title = equilibration nvt (invacuo) ; define = -DFLEXIBLE ; ;Run parameters integrator =

Re: [gmx-users] generating full atomic structure

Hi, There are some suggestions on the GROMACS website. Mark On 13/04/2015 9:01 am, "Ming Tang" wrote: > Dear all, > > I got a pdb file including the C-alpha itoms of different residues only. > Is there any software that can add the other atoms of the residues to the > pdb file automatically? >

Re: [gmx-users] In-Vacuo ligand only equilibration (Iris Nira Smith)

On 4/13/15 10:38 AM, Iris Nira Smith wrote: Thank you Justin for your insight to your previous response. I made adjustments to my equilibration .mdp file (below) to run as NVT in vacuo. Can you review and advise on corrections? Looks fine (don't use -DFLEXIBLE for MD in general, but it only

[gmx-users] Bootstrap error

Dear All I am new to Gromacs and i am trying to install it in Ubuntu. I am getting following error while using the command ./configure in cmake step. C compiler on this system is: cc Error when bootsratpping CMake: Cannot find appropriate C++ compiler on this system. Please specify one using env

Re: [gmx-users] Bootstrap error

Hi, You don't need to compile the latest CMake on Ubuntu, you can use the version available in the apt package management system. But you will need a C++ compiler for recent versions of GROMACS, so get the latest gcc for your Ubuntu version while you are doing that. Mark On Mon, Apr 13, 2015 at

Re: [gmx-users] about GPU acceleration

Yes. -- Szilárd On Fri, Apr 10, 2015 at 12:42 PM, BIRD wrote: > Dear all > Does the new Gromacs5 support the SHIFT for Lennard Jones and Coulombic > interactions by GPU acceleration? > thank you > Cao Ph.D > > > Nankai University > Tianjin China > -- > Gromacs Users mailing list > > * Please s

[gmx-users] How to call an external LAPACK function in gromacs

Dear All, I am a new user of gromacs 5.0. For my own purposes I made small changes in a gromacs source code where I called a function named "DPOTRF". This is a standard function in LAPACK library but not in the gromacs internal LAPACK library. Now I have a problem of compiling. What I did is: cm

[gmx-users] Clusters

Are there any tutorial or tips to use cluster in Gromacs? I have 5 nodes with 9 cores each node and want use all them in one simulation, is that possible? I've read something about gromacs MPI but I don't know how to use. Can someone suggest some text or some tutorial for me? Thanks in advance

Re: [gmx-users] Clusters

What network do you have? Unless it's fast (that is low latency) you won't be able to run across nodes. Are you sure about 9 cores, that number seems strange? -- Szilárd On Mon, Apr 13, 2015 at 11:52 PM, Lucas Dadalt Morero wrote: > Are there any tutorial or tips to use cluster in Gromacs? > I h

Re: [gmx-users] Number of hardware threads does not match OpenMP

Hi, The former warning is the direct consequence of the latter. Your job scheduler or MPI launcher is setting process affinity; as a result the OpenMP library reports 1 CPU in contrast with the 20 CPUs/cores that our low-level detection reports. You could be loosing a considerable amount of perfor

Re: [gmx-users] CNT force field and simulation

Hi Pierre, Two things: 1. rtp entries are pretty useless for crystal structures. Biochemical simulations use molecules with a precise atomic composition, so an rtp template makes sense. Not for crystals. Your rtp entry contains useless information and the only thing in your coordinates that can f

Re: [gmx-users] CNT force field and simulation

Also, I would really suggest that you read the Gromacs manual on the subject of topology. This is extremely useful, because there is a philosophical clash between biomolecular simulations and solid-state simulations in terms of the concept of connectivity. You are effectively using a tool that is b

Re: [gmx-users] Clusters

Sorry, it's 8 cores. Network is good. The hardware setup is ok, I just want to know how to perform a gromacs simulation using all the nodes.. Lucas > Date: Tue, 14 Apr 2015 02:06:49 +0200 > From: pall.szil...@gmail.com > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Clusters > > What ne

[gmx-users] Post-Processing on the REMD trj

Dear users, Rescently, I used REMD to do some simulation by Gromacs , I konw GROMACS exchanges coordinates. So does this means every trajectory was written at a temperture ?AND if i want to analyse the lowest temperature, can I just analyse md0.xtc as 'trajectory no longer be continuous'(http

Re: [gmx-users] A simple question

Dear Dr.Smith , Thanks for your replay . This is a part of my PDB file :  ATOM      1  CD1 TRP      1      19.910  19.430  16.500  1.00  0.00ATOM      2   CD1 TRP      1      20.210  20.850  16.560  1.00  0.00ATOM      3  CD1 TRP       1      19.010  21.540  16.970  1.00  0.00ATOM      4  CD1 TRP  

Re: [gmx-users] POPE lipid from Tieleman's web site, the box of xy dimension will shrink during the simulation

Dear Justin; Thanks for your reply! Maybe I will use other kind of lipid or force field instead. Sciences: Nie Xuechuan At 2015-04-12 04:09:24, "Justin Lemkul" wrote: > > >On 4/11/15 8:25 AM, niexuechuan wrote: >> Dear all, I am new to lipid simulation. I have downloaded the

Re: [gmx-users] POPE lipid from Tieleman's web site, the box of xy dimension will shrink during the simulation

Dear Thomas; Thanks for your suggestion. I will try for it. Sciences: Nie Xuechuan At 2015-04-12 04:34:18, "Thomas Piggot" wrote: >Justin is right about the parameters being sub-optimal, for example see: > >de Vries et al. http://pubs.acs.org/doi/abs/10.1021/jp0366926 > >which I

Re: [gmx-users] Bootstrap error

Thank you very much. Sent from my iPhone > On 13-Apr-2015, at 11:24 pm, Mark Abraham wrote: > > Hi, > > You don't need to compile the latest CMake on Ubuntu, you can use the > version available in the apt package management system. But you will need a > C++ compiler for recent versions of GROM

Re: [gmx-users] A query

Thank you all for the reply. On Mon, Apr 13, 2015 at 6:39 PM, Mark Abraham wrote: > Hi, > > Yes, there are a few programs in computational chemistry that give such > quotes randomly; GAUSSIAN comes to mind. There's an environment variable > described in one of the manual appendices that will dis

[gmx-users] adding SR2++ to charm27 force field

Dear all, I am trying to add SR 2++ in charm27 force field. I modified the ffnonbonded.itp, ffnanonbonded.itp, ions.itp, aminoacids,rtp, atomtypes.atp according to the parameters of SR in oplsaa.ff. However, when using pdb2gmx, I came across the following fatal error: Atomtype SR not found. Coul

Re: [gmx-users] Number of hardware threads does not match OpenMP

Dear Szilárd, Thanks for your reply. I'll try your proposed fix. I was also wondering if the simulations performed could be affected in terms of reliability and accuracy or not (ie. do I need to redo the simulations already performed with the corrected settings)? Thanks! Dries -- Gromacs Users