[gmx-users] Trajectory correction for pbc before H-bond analysis

Dear Users, I always do pbc correction for the trajectory before doing RMSD, Radius of Gyration and COM separation analysis for my protein-ligand complex. Is pbc correction recommended before doing H-bond analysis ? I have 20 long simulations and I need to do a quick H-bond analysis for them.

[gmx-users] Fourier dihedral potential: typo or correct?

Dear all: In manual-5.06, page:82, [image: Inline image 1] Shouldn't the last term be C4(1-cos(4Phi)) ? --Masrul -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Can I fix two of the cubic cell dimensions during an NPT simulation?

Justin, that’s awesome. Thanks On 14/03/2016 22:34, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul" wrote: > > >On 3/14/16 6:31 PM, Nash, Anthony wrote: >> Hi all, >> >> Is there a

Re: [gmx-users] Can I fix two of the cubic cell dimensions during an NPT simulation?

On 3/14/16 6:31 PM, Nash, Anthony wrote: Hi all, Is there a way of keeping the x, y box dimensions fixed during an NPT simulation, with changes to volume only changing in the Z dimension? Semiisotropic is not quite working out, see below. Context: I want a coiled-coil dimer aligned in the

[gmx-users] Can I fix two of the cubic cell dimensions during an NPT simulation?

Hi all, Is there a way of keeping the x, y box dimensions fixed during an NPT simulation, with changes to volume only changing in the Z dimension? Semiisotropic is not quite working out, see below. Context: I want a coiled-coil dimer aligned in the Z direction. Each coiled-coil will see it¹s

Re: [gmx-users] flat-bottom reference file format

On 3/14/16 4:20 PM, Jinmei Wang wrote: dear list, I want to restrain a group of atoms within one sphere. I got the sphere center coordinate using g_traj In topol.top I added this part: #ifdef POSRES_FLATBOTTOM [ position_restraints ] ; i funct gr(nm)k (kJ/mol/nm)

[gmx-users] flat-bottom reference file format

dear list, I want to restrain a group of atoms within one sphere. I got the sphere center coordinate using g_traj In topol.top I added this part: #ifdef POSRES_FLATBOTTOM [ position_restraints ] ; i funct gr(nm)k (kJ/mol/nm) 4211.5 30

[gmx-users] how to use gmx rdf to compute the RDF between the COMs of molecules (more than 3)

Dear GROMACS users, Recently, I am trying to compute the RDF between the COMs of five molecules using gmx rdf. The detailed command I wrote is as follows: gmx rdf -f *.xtc -s *.tpr -n *.ndx -b * -e * -rdf mol_com -norm -o rdf.xvg I've made an index file of a group formed by the five

Re: [gmx-users] Problem with the mdrun_openmpi on cluster

On 3/14/16 1:26 PM, James Starlight wrote: For that system I have not defined virtual sites. That disagrees with the error message, which explicitly complains about vsites. BTW the same simulation on local desctop using 2 cores from core2 duo runs OK =) Because you're not invoking DD

Re: [gmx-users] Problem with the mdrun_openmpi on cluster

For that system I have not defined virtual sites. BTW the same simulation on local desctop using 2 cores from core2 duo runs OK =) so one of the solution probably is to try to use more recent gmx 5.0 to see what will happenes 2016-03-14 18:22 GMT+01:00 Justin Lemkul : > > > On

Re: [gmx-users] Problem with the mdrun_openmpi on cluster

On 3/14/16 1:19 PM, James Starlight wrote: I tried to increase size on the system providding much bigger bilayer in the system for this task I obtained another error also relevant to DD Program g_mdrun_openmpi, VERSION 4.5.7 Source code file:

Re: [gmx-users] Problem with the mdrun_openmpi on cluster

On Mon, Mar 14, 2016 at 5:26 PM, James Starlight wrote: > the error is likely when I try to run not very big system on large > number of CPUs in parallel > > > my system is receptor embedded within the membrane consisted of 120 lipids > that was produced by grompp > >

Re: [gmx-users] Problem with the mdrun_openmpi on cluster

I tried to increase size on the system providding much bigger bilayer in the system for this task I obtained another error also relevant to DD Program g_mdrun_openmpi, VERSION 4.5.7 Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec_con.c, line: 693 Fatal error: DD cell 0 2

Re: [gmx-users] Can't do parallell free energy calculation with couple_intramol=no -- workaround?

Hi Michael, Great, thanks for the feedback! Good point about OMP_NUM_THREADS being set in the environment; it is often possible to set the "width" or "depth" of the ranks in the scheduler, which will often set the desired OMP_NUM_THREADS (instead of assuming 1) which makes sure that no override

Re: [gmx-users] Can't do parallell free energy calculation with couple_intramol=no -- workaround?

Hi Szilard, I tested running with OpenMP parallelization in gromacs 5.1.2 and it solves the problem. Thanks for your advice! I also found that it is necessary to do deactivate the OMP_NUM_THREADS environment variable "unset OMP_NUM_THREADS" prior to running gromacs, since if this variable is

Re: [gmx-users] Problem with the mdrun_openmpi on cluster

also below my mdp options which might be relevant- I am using here a MArtini ff of the system for simulating of GPCR embedded within lidips. title = production run for GPCR dt = 0.02 nsteps = 5 nstxout = 0 nstvout = 0 nstlog

Re: [gmx-users] Problem with the mdrun_openmpi on cluster

forgot to add that I tried to decrease number of CPUs to 16 and error was the same 2016-03-14 17:26 GMT+01:00 James Starlight : > the error is likely when I try to run not very big system on large > number of CPUs in parallel > > > my system is receptor embedded within the

Re: [gmx-users] Problem with the mdrun_openmpi on cluster

the error is likely when I try to run not very big system on large number of CPUs in parallel my system is receptor embedded within the membrane consisted of 120 lipids that was produced by grompp Initializing Domain Decomposition on 64 nodes Dynamic load balancing: no Will sort the charge

Re: [gmx-users] Problem with the mdrun_openmpi on cluster

What is your box size (x, y, z)? What happens if you use half that number of nodes? === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics

[gmx-users] Problem with the mdrun_openmpi on cluster

Hello, I am trying to submit job on 64 nodes on mu local cluster using below combination of software DO="mpiexec -np 64" PROG="g_mdrun_openmpi" $DO $PROG -deffnm sim obtaining error Program g_mdrun_openmpi, VERSION 4.5.7 Source code file:

Re: [gmx-users] Relative binding free energy

On Mon, 14 Mar 2016 14:08:32 + Stefania Evoli wrote: > Please, could you give a look at that? I obtained it by using the > useful tool described in the article 'A Python tool to set up > relative free energy calculations in GROMACS¹ Pavel V. Klimovich and > David

[gmx-users] Suggestions on running simulations of very long polypeptide chains

Hi all, I¹m looking to run MD simulations of regions of a collagen molecule. A whole collegen molecule is made up of three polypeptide chains, each around 1000 residues long (gross generalisation as there are around 24 different collagen protein families). I am only interested in modelling a

Re: [gmx-users] Vizualization of lipid protein system

Right, thank you! probably I need to combination of -pbc mol and -pbc nojump in the sequence order. 2016-03-14 12:57 GMT+01:00 Justin Lemkul : > > > On 3/14/16 7:55 AM, James Starlight wrote: >> >> I guess for my case this should work >> >> 3 If you want jumps removed, extract

Re: [gmx-users] Relative binding free energy

Thank you for your time and precious help. The complete topology is #include "amber99sb.ff/forcefield.itp" ; Gly_GMX.top created by acpype (Rev: 403) on Wed Jan 20 13:39:56 2016 ;[ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 2 yes

[gmx-users] Error with gmx dielectric

Dear All, before sending a post to gmx-developers, I would like to know if someone else has my same problem. When executing "gmx dielectric …." on a simulation, after having produced the dipole correlation file with "gmx dipoles -corr total -P 2 ….", I get the following error: *** Error in

Re: [gmx-users] Relative binding free energy

I had a quick look at this and I see quite a few problems there. You don't show the [atomtypes] but I suppose that whatever you call *_dummy has zero vdW parameters. BTW, there is no need to invent different atom type names for every dummy as their non-bonded parameters are all zero anyway and

Re: [gmx-users] Query about a simple MD with constant electric field

Dear Erik, yes, that was the problem. I set comm-mode = none and now it works also without PME and for non-neutral systems Thank you very much Ivan On 2016-03-14 10:50, Erik Marklund wrote: Dear Ivan, It works also without PME and for non-neutral systems. What are your COM-removal

Re: [gmx-users] Relative binding free energy

The output looks like that Steepest Descents did not converge to Fmax < 100 in 2501 steps. Potential Energy = -1.80220751343547e+05 Maximum force = 1.22489147313117e+03 on atom 1 Norm of force = 1.73979807081018e+01 The structure seems not modified. When I mentioned ‘do not work’ I

Re: [gmx-users] Vizualization of lipid protein system

On 3/14/16 7:55 AM, James Starlight wrote: I guess for my case this should work 3 If you want jumps removed, extract the first frame from the trajectory to use as reference, and then use trjconv -pbc nojump with that first frame as reference hovewer in my case the VMD movie looks like all

Re: [gmx-users] Vizualization of lipid protein system

I guess for my case this should work 3 If you want jumps removed, extract the first frame from the trajectory to use as reference, and then use trjconv -pbc nojump with that first frame as reference hovewer in my case the VMD movie looks like all solvent molecules are spread from the protein in

Re: [gmx-users] Vizualization of lipid protein system

forgot to add if I use -fit rot+trans the system looks fine BUT moves as a whole like a propeller =)) J. 2016-03-14 12:48 GMT+01:00 James Starlight : > Dear all! > > I am looking for the possibility to vizualize my long md trajectory > for the receptor embedded in the

Re: [gmx-users] Vizualization of lipid protein system

On 3/14/16 7:48 AM, James Starlight wrote: Dear all! I am looking for the possibility to vizualize my long md trajectory for the receptor embedded in the membrane If I just load the trajectory to vmd there is no problem with the exeption that receptor moves laterally along the membrane

[gmx-users] Vizualization of lipid protein system

Dear all! I am looking for the possibility to vizualize my long md trajectory for the receptor embedded in the membrane If I just load the trajectory to vmd there is no problem with the exeption that receptor moves laterally along the membrane resulting at the end in PBC artifacts If It try to

Re: [gmx-users] Relative binding free energy

How does the final structure for lambda=0 minimisation look like? This may give you a hint as to what is wrong. What exactly does "do not work" mean? That's not very descriptive... It may help a lot to actually post the relevant A and B columns from your topologies. Single topology means in

Re: [gmx-users] tpo is removed....

On 3/14/16 6:37 AM, Mehreen Jan wrote: respected sir! sorry for disturbing thank you for provided guide line i used following perameters... gromacs 5.0.7 force field 43A1p (which is downloaded from given gromacs web) problem: after 1ns i stop the simulation ang generate PDB of my protein. i

Re: [gmx-users] Relative binding free energy

The minimization crush after 1182 steps like follow Step= 1116, Dmax= 1.2e-02 nm, Epot= -1.76932e+05 Fmax= 9.54828e+03, atom= 1 Step= 1117, Dmax= 1.4e-02 nm, Epot= -1.77307e+05 Fmax= 2.85691e+04, atom= 8 Step= 1119, Dmax= 8.6e-03 nm, Epot= -1.99060e+05 Fmax= 3.84768e+07, atom= 8 Step= 1124, Dmax=

Re: [gmx-users] Simulation of the membrane protein using Martini. MDP options

The question in mdp options is here gen_vel = no gen_temp = 320 gen_seed = 473529 according to the central idea during equilibration I should to use gen_vel = yes to generate initial velocities ensemble. however in that case

[gmx-users] tpo is removed....

respected sir! sorry for disturbing thank you for provided guide line i used following perameters... gromacs 5.0.7 force field 43A1p (which is downloaded from given gromacs web) problem: after 1ns i stop the simulation ang generate PDB of my protein. i found that my TPO is removed from PDB

Re: [gmx-users] How Gromacs h_bond module compute hydrogen correlation function ?

Hi, Gromacs uses FFTs to calculate C(t), exploiting that convolutions (such as an autocorrelation) turns into simple muliplications in Fourier space. If you are interested in the details, have a look at gmx_hbond.c. In the function do_hbac(), look for the last call to low_do_autocorr() and the

Re: [gmx-users] Simulation of the membrane protein using Martini. MDP options

Hi, If you're using Gromacs 5.x, I suggest using the mdp options from these files: http://md.chem.rug.nl/index.php/mdp5 The paper associated with these is here: http://www.sciencedirect.com/science/article/pii/S0010465515003628 Best regards Marlon Sidore PhD Student Laboratoire d'Ingénierie

[gmx-users] Simulation of the membrane protein using Martini. MDP options

Hi, I am trying to use MARTINI ff for simulation of membrane protein. Two questions regarding mdp options for such runs 1) May I use below options taken from the Justin tutorial with the MARTINI ff ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5; 10 fs rlist =

Re: [gmx-users] problem in editing .eps file of hbond

Dear Shahid, No. You need to post-process the xpm/ndx yourself. Kind regards, Erik > On 13 Mar 2016, at 08:58, Shahid Nayeem wrote: > > Is it really possible in g_hbond to get hbmap.xpm for plotting only those > hydrogen bonds between chain A and chain B of protein which

Re: [gmx-users] Query about a simple MD with constant electric field

Dear Ivan, It works also without PME and for non-neutral systems. What are your COM-removal settings? They can certainly mess up an accelerating system. Kind regards, Erik > On 10 Mar 2016, at 10:33, Ivan Gladich wrote: > > Dear Prof. Spoel > first of all thank you for

[gmx-users] Relative binding free energy

Dear Users, I’m performing relative binding free energy by using Gromacs 5.0.5. As I understood reading the sections 5.3.4, 6.1 and 7.3.23 of the GROMACS 5.0.5 manual I should avoid to use couple-moltype and couple-lambda0/couple-lambda1 because they would override the A and B states, already