Re: [gmx-users] NVT.gro is not genetared

Hi, see the log file for more information and correct the error, it is not recommended to use -maxwarn without knowing the real problem. or share the log file here. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] NVT.gro is not genetared

Dear gmx-users, I'm doing a simulation to a potein- DPPC bilayer system. When tried to run NVT after energy minimization, the following error occurs. --- Program gmx grompp, VERSION 5.1.4 Source code file:

[gmx-users] how we can use Amber ff that are frcmod.hem not present in gromacs

hello everyone i have amber force field for Heme fe---o2 is it possible to convert it to gromacs or we use it as it is in gromacs if we use it then how -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?

This community is mostly focused on other things. If you have solid silica under a non-native (to Gromacs) forcefield and all the bonded parameters have been copied correctly, there may be issues with your partial charges, LJ parameters, and mixing rules. Also make sure your original

[gmx-users] Anybody using Silica InterfaceFF on Gromacs?

Hi, I converted the InterfaceFF silica parameters to use in Gromacs (and to be compatible with the AMBER forcefield) and have gotten some problems, namely I am getting a slightly bigger equilibrium bond length than I should. I was wondering if there were other Gromacs users out there that have

[gmx-users] Deform a liquid

Hi I am new to gromacs and so a basic doubt. How do we use 'deform' as specified in non equilibrium section of mdp file? Considering I have a box of polymer to be given some shear only in x direction, what should be the arguments? -- Nishi Kashyap Undergraduate Chemical Engineering IIT Delhi --

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

I have read both things thoroughly. I am new to this and so having a hard time gathering basic concepts. So, correct me if I am wrong: To calculate shear viscosity in a PEG system: 1. Created a stable system and given cos_acceleration =0.05 2. Since I would know A(amplitude of acceleration),rho

Re: [gmx-users] Atom types comparison between CGenFF and Charm36FF

Thanks, Justin. Sure. On Wed, Jun 28, 2017 at 10:21 AM, Justin Lemkul wrote: > > > On 6/28/17 9:10 AM, Mohsen Ramezanpour wrote: > >> Thanks Justin for your comment. >> >> I have a bit of difficulty for the finding the analog parts to these two >> parts. >> >> Is there any

Re: [gmx-users] Atom types comparison between CGenFF and Charm36FF

On 6/28/17 9:10 AM, Mohsen Ramezanpour wrote: Thanks Justin for your comment. I have a bit of difficulty for the finding the analog parts to these two parts. Is there any database (preferably with shapes) for the molecules available in charmmFF? The CHARMM topology files have full residue

Re: [gmx-users] gmx wham problem

It looks like you need to sample more states, 13 is not enough. Probably more like 20-30+ would be needed to get a smooth PMF as is discussed in that tutorial. The weird features in your PMF are from insufficiently overlapping histograms, for example the bump near -2.2 nm corresponds to having

[gmx-users] gmx wham problem

dear all, I am studying the affinity between an antibody and an amyloid peptide; I am interested in the evaluation of the PMF. I have a problem with the PFM shape. I followed the protocol described in the umbrella-sampling tutorial

Re: [gmx-users] Atom types comparison between CGenFF and Charm36FF

Thanks Justin for your comment. I have a bit of difficulty for the finding the analog parts to these two parts. Is there any database (preferably with shapes) for the molecules available in charmmFF? Cheers, Mohsen On Tue, Jun 27, 2017 at 7:51 PM, Justin Lemkul wrote: > > >

Re: [gmx-users] (no subject)

Anyone if have idea, Kindly address On 28 Jun 2017 07:41, "Shivangi Agarwal" wrote: > Dear all gromacs users > > i have to define a new residue, i have added it in *residuetype.dat* file. > but still getting error: "residue type not found". > Kindly suggest > -- >

[gmx-users] Pram file to gromac converter

Is there any park file converter that convert pram file of amber into gromacs -- 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 http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] Pullin dhiedral angle version 2016

Hello, I’m trying to use the pull code in my RNA system. After a week I was finally able to make it work. But I have some problems This is what I wanted to do: In my system I have a bulge and I would like to se what happen to the rest of the structure if the bulge is completely outside from the

Re: [gmx-users] Protein-ligand binding Cut-offs

I want to see the closest binding glycine molecules so would "within x distance of any protein atom" be more appropriate? Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark

Re: [gmx-users] Number of Contacts

Hi, I used the following command.. gmx mindist -f ../traj_comp3.xtc -s ../md3.tpr -n index.ndx -od minidist.xvg -on numb_count -d 0.65 By doing this I got this numb_count.xvg graph here https://drive.google.com/open?id=0B99qIEZlZSXfVnQxY3JsUm1rRnc In this number of contacts varying up to 500

Re: [gmx-users] use INTERFACE Force Field

Ok, I did a bit of reading and it may be usable in GROMACS as is. However that doesn't mean that it will be easy to build the topology, as pdb2gmx may not know how to read/work with it. At least the potential energy function is compatible with GROMACS, so that's good news. /J On Wed, Jun 28,

Re: [gmx-users] use INTERFACE Force Field

If only it was that straightforward. I am not familiar with this INTERFACE ff, but this is not just about format and layout. There's much more at stake. However, the team behind it appears to be planning to port it soon: "Developments in progress include a graphical user interface to construct

Re: [gmx-users] Protein-ligand binding Cut-offs

Hi, You get to choose... do you want everything within some distance of the protein center of mass, or any protein atom, or something else. But don't be suprrised if there are no ligand atoms super close to the protein center of mass ;-) Mark On Wed, Jun 28, 2017 at 12:47 PM Pandya, Akash

Re: [gmx-users] use INTERFACE Force Field

Hello, Possible bot not easy.Look into Gromacs folder share/top/ all force fields sit there as text files your will have to make ITERFACE text files in same format and layout.What you download as ITERFACE force field are also text files with parameters, but layout is for different programs.

[gmx-users] use INTERFACE Force Field

Dear gmx users, I would like to use gromacs 5.1v with INTERFACE force field. Please, any advice and suggestions, thank you. Best regards, Miji -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] Protein-ligand binding Cut-offs

I assumed it meant to select all ligand molecules closest to the protein's centre of mass. I'm not entirely sure if that is correct interpretation. Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] Protein-ligand binding Cut-offs

How are you interpreting "within 4A of my protein?" What has your protein's center of mass got to do with it? Mark On Wed, Jun 28, 2017 at 12:16 PM Pandya, Akash wrote: > Yes it is. So that means I need a cut-off greater than right? > > Akash > > -Original

Re: [gmx-users] Protein-ligand binding Cut-offs

Yes it is. So that means I need a cut-off greater than right? Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 28 June 2017 11:08 To: gmx-us...@gromacs.org

Re: [gmx-users] Protein-ligand binding Cut-offs

Is the radius of your protein greater than 0.4 nm? Mark On Wed, 28 Jun 2017 12:05 Pandya, Akash wrote: > Hi, > > I want to select all the ligands in my box within 4A of my protein. I > looked at gmx help select and I used the command below but nothing > appeared. It

Re: [gmx-users] Protein-ligand binding Cut-offs

Hi, I want to select all the ligands in my box within 4A of my protein. I looked at gmx help select and I used the command below but nothing appeared. It didn't show my default groups which correspond to the "14" for ligand and "1" for protein. Please advise me on what to do? Am I missing

Re: [gmx-users] adding a custom residue with an itp file

Thanks, Justin. I suspected that was the case but I wanted to be 100% sure :D .Jose On Tue, Jun 27, 2017 at 9:48 PM, Justin Lemkul wrote: > > > On 6/27/17 12:32 PM, Jose Borreguero wrote: > >> Dear Gromacs users, >> >> I have created an include topology file (sil.itp) for a

Re: [gmx-users] gmx spatial

Yes, you are right, but the problem is that if I visualize the trajectory I have the solute around the protein whereas with the spatial distribution function I obtain density function around the protein as well as within the protein core and this make no sense or at least is not convincing.