Re: [gmx-users] using the Fourier function for dihedral in the OPLS FF

On 6/2/17 7:31 PM, Saeed Nasiri wrote: Dear Justin I really thanks for your useful help in the last topic. I totally changed the method. I copy the oplsaa.ff file in the working directory and insert the parameters in the related files. But I have a problem with dihedral parameters. As far as

Re: [gmx-users] Calculation of nematic order parameter using gromacs

Hi Nidhi, In short: you are using a general-purpose software, so it does not have tools for all specific applications any user might be interested in. Either you have to hack/adapt existing analysis tools or you have to write your own tools. That being said: the director is a rather arbitrary

Re: [gmx-users] Calculation of nematic order parameter using gromacs

On Sat, 3 Jun 2017, nidhi sorout wrote: Hello, Thank you Antonio.. But my angle of interest is the angle between the molecular axis of protein and the director. I am not able to understand here, from where I can choose this 'director'? In your case, what does 'director' mean exactly?

[gmx-users] using the Fourier function for dihedral in the OPLS FF

Dear Justin I really thanks for your useful help in the last topic. I totally changed the method. I copy the oplsaa.ff file in the working directory and insert the parameters in the related files. But I have a problem with dihedral parameters. As far as I know, the opls force filed used the

Re: [gmx-users] Umbrella sampling and PMF calculations

> > >> > A pull vector can indeed not be (0, 0, 0) but that's not a pull rate. The pull vector is exactly as set by you to N N Y, maybe the code multiplies the vector components by the corresponding pull rates and then checks the resulting velocity vector, I don't know, but the error is there

Re: [gmx-users] Umbrella sampling and PMF calculations

On 6/2/17 6:40 PM, Alex wrote: I find that surprising. Please provide the full, exact error and your pull settings. All of the geometries should work with zero or non-zero pull rates. But I admit, it has been many years since I used GROMACS with the pull code. Simply take your pull

Re: [gmx-users] Umbrella sampling and PMF calculations

> > I find that surprising. Please provide the full, exact error and your >> pull settings. All of the geometries should work with zero or non-zero >> pull rates. But I admit, it has been many years since I used GROMACS with >> the pull code. >> > Simply take your pull code from the tutorial and

Re: [gmx-users] charmm36 lipid forcefield error

On 6/2/17 3:13 PM, Archana Sonawani-Jagtap wrote: Thanks for solving my error. But then do we need to remove the periodicity of the bilayer obtained from charmm-gui? Have you visualized the structure you got? Is there a reason you think you need to play with trjconv yet? -Justin --

Re: [gmx-users] Randomly replace molecules with another molecule

On 6/2/17 3:51 PM, Li, Shi wrote: Dear Gromacs users, I am wondering if there is a better way to randomly replace some molecules in a system box with another type of molecule. For example, I have a system with 1000 molecule A as the solvent and I have another molecule B as the solute. I want

Re: [gmx-users] Umbrella sampling and PMF calculations

On 6/2/17 4:17 PM, Alex wrote: So, Justin, just to follow up here. With 'cylinder', grompp refuses to accept a zero pulling rate. This begs a different question: in my I find that surprising. Please provide the full, exact error and your pull settings. All of the geometries should work

Re: [gmx-users] Calculation of nematic order parameter using gromacs

Hello, Thank you Antonio.. But my angle of interest is the angle between the molecular axis of protein and the director. I am not able to understand here, from where I can choose this 'director'? Nidhi On 30 May 2017 8:55 p.m., "Antonio Baptista" wrote: > Hi Nidhi, > >

Re: [gmx-users] Umbrella sampling and PMF calculations

So, Justin, just to follow up here. With 'cylinder', grompp refuses to accept a zero pulling rate. This begs a different question: in my particular system, the COM position coincides with the center of the single reactive pore at the geometric center of the membrane. Why even bother with this

Re: [gmx-users] Using SLLOD to find Viscosity

On 02/06/17 22:02, nishi kashyap wrote: Hi I have a system of PEG for which I want to find viscosity. I want to use SLLOD equations to find viscosity for a specific shear rate. I have read allot about different ways , even tried to use 'deform'. But I did not understand what do you mean by "off

[gmx-users] Using SLLOD to find Viscosity

Hi I have a system of PEG for which I want to find viscosity. I want to use SLLOD equations to find viscosity for a specific shear rate. I have read allot about different ways , even tried to use 'deform'. But I did not understand what do you mean by "off diagonal elements in a single array". I am

[gmx-users] Randomly replace molecules with another molecule

Dear Gromacs users, I am wondering if there is a better way to randomly replace some molecules in a system box with another type of molecule. For example, I have a system with 1000 molecule A as the solvent and I have another molecule B as the solute. I want to generate a series of systems with

Re: [gmx-users] charmm36 lipid forcefield error

Thanks for solving my error. But then do we need to remove the periodicity of the bilayer obtained from charmm-gui? Regards, Archana On Fri, Jun 2, 2017 at 2:24 AM, Justin Lemkul wrote: > > > On 6/1/17 4:43 PM, Archana Sonawani-Jagtap wrote: > >> Hi, >> >> I want to perform

Re: [gmx-users] Umbrella sampling and PMF calculations

Yes, because if your ion diffuses laterally (or whatever constitutes your "hole"), then you're not sampling what you think you're sampling. That's what the cylinder geometry is for. You have a system capable of significant lateral movement, so if you fail to apply a bias that acts in

Re: [gmx-users] Interpretation of RMSD matrix

Hi, I suggest you decide what you want to observe before choosing a tool to observe with :-) A telescope is no good for micro-organisms. Mark On Fri, 2 Jun 2017 17:20 Apramita Chand wrote: > Dear All, > I would be grateful if you could help me with links to relevant

[gmx-users] Interpretation of RMSD matrix

Dear All, I would be grateful if you could help me with links to relevant papers/websites/sources on how to interpret RMSD matrices when comparing all frames of single trajectory to reference structure and also when comparing two different trajectories. I am taking the reference structure from

[gmx-users] Peptide out of box even after applying trjconv

Dear All, Even after applying g_trjconv -f file.gro -s file.tpr -pbc mol -ur compact -center -o newfile.gro, for visualisation purposes of peptide inside the box, a portion of it still sticks out of the box. Is it unnatural? What might be done to sort out the problem? yours sincerely Apramita

[gmx-users] Problem with center-of-mass RDF and subsequent coordination number calculation

Dear All, I want to calculate the COM RDFs between my peptide and water for which I have used the -com option in gromacs.(Also tried with -com and -rdf res_com). It generates a wierd RDF which does not look correct. I want to take the first minimum and use the -cn option to get the coordination

Re: [gmx-users] Doubt about gmx wham analysis

On 6/2/17 7:20 AM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, I would like to correct myself. Actually, the COM of the two groups - Protein and Ligand are about 5 nm away at the end of the pulling process. But the rear end of the ligand is just 0.6 nm away from the closest Amino acid

Re: [gmx-users] System volume "jumps" on exact continuations

Thanks, I've opened the issue at https://redmine.gromacs.org/issues/2200 . From: Mark Abraham Sent: Thursday, June 1, 2017 20:10 To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] System volume

Re: [gmx-users] Doubt about gmx wham analysis

Dear Justin, I would like to correct myself. Actually, the COM of the two groups - Protein and Ligand are about 5 nm away at the end of the pulling process. But the rear end of the ligand is just 0.6 nm away from the closest Amino acid of the Protein. Is that reasonable for the Binding

Re: [gmx-users] destruction of the structure of a molecule in water after energy minimization

On 6/2/17 4:26 AM, Saeed Nasiri wrote: Dear *Justin* I checked all of the parameters again and again and I try that to prepare them similar to the opls itp files. However, the problem does not solve. Also, when the energy minimization has been run there is warning about 1-4 interaction. I

Re: [gmx-users] How to improve the performance of simulation in HPC (finding optimal number of nodes and processors)

I suggest that you try to understand the parallelization option of mdrun first. You seem to be mixing MPI and thread-MPI. The latter won't work for multi-node runs. If you sort that out and launch with correctly set up PBS parameters (ranks and cores/threads per ran), your runs should be fine.

Re: [gmx-users] Doubt about gmx wham analysis

On 6/1/17 6:29 PM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, Since I have the settings pull_coord1_dim = Y Y Y, I am not sure which axis the ligand is pulled. My initial simulation box size was 5 nm in each side. To care of the pulling of the ligand in any direction I made the box

Re: [gmx-users] Umbrella sampling and PMF calculations

On 6/1/17 6:35 PM, Alex wrote: You have a membrane with water on either side, yes? That's a layered system. But frankly, at this point I don't follow at all what you're trying to do. - Let me try from the beginning. :) A membrane in XY, water on both sides. At the center of the

Re: [gmx-users] How to improve the performance of simulation in HPC (finding optimal number of nodes and processors)

Perhaps try something like: (in your PBS Script) -l nodes=8:ppn=28 (request for 8 nodes with all cores) source (your source stuff here) mpirun -n 56 -npernode 7 gmx_mpi mdrun -ntomp 4 (your run stuff here). This should give you 7 mpi ranks per node, with each rank using 5 openMP threads, which

Re: [gmx-users] Perturbation Thermodynamic Integration

What I notice is: You don't use bond-constraints but you have set your time step to 2 fs. What happens if you (significantly) increase simulation time per lambda? Your variances are really large. What is the motivation of using such a long cutoff radius for vdW? On Fri, 26 May 2017 11:13:08

[gmx-users] destruction of the structure of a molecule in water after energy minimization

> > Dear *Justin* > > I checked all of the parameters again and again and I try that to prepare > them similar to the opls itp files. > However, the problem does not solve. Also, when the energy minimization > has been run there is warning about 1-4 interaction. I think > that the problem is