[gmx-users] GLYCAM for gromacs

Dear gmx users, We are trying to simulate polysaccharides, cellulose and hemicellulose in particular, in GROMACS. The intention is to use GLYCAM forcefield parameters as well. My question is, is there any properly quick way to parametrize GLYCAM force field to be used in GROMACS? More

Re: [gmx-users] ACPYPE not working.

Have you tried to source amber before commanding acpype for the conversion? Apparently it’s looking for antechamber but it can’t access it. When amber is sourced first, you can get a result from commands such as antechamber -h Try to first source your amber, and then run acpype. > On 1 Nov 2018,

[gmx-users] pdb2gmx fatal error

Dear gmx users, I am trying to simulate a cellobiose, using GROMOS53a6CARBO. The atom names were modified according to the rtp file of the force field. Yet, I get the following error while I perform pdb2gmx command: Fatal error: Residue 4 named GLC of a molecule in the input file was mappe

Re: [gmx-users] pdb2gmx fatal error

mx-us...@gromacs.org Subject: Re: [gmx-users] pdb2gmx fatal error On 11/7/18 1:05 PM, Ali Khodayari wrote: > Dear gmx users, > > > > I am trying to simulate a cellobiose, using GROMOS53a6CARBO. The atom > names were modified according to the rtp file of the force field. Yet, > I get t

Re: [gmx-users] pdb2gmx fatal error

Dear Justin, Thank you for your full explanation. That made it all clear now. Kind regards, Ali > On 13 Nov 2018, at 00:57, Justin Lemkul wrote: > > > > On 11/8/18 1:37 PM, Ali Khodayari wrote: >> Dear Justin, >> >> Thank you for your response. Yet,

[gmx-users] make_ndx and assigning velocities

Dear Gmx users, I have two questions. I am wondering how I can assign residues from different chains to one single index group? Say, residues 50 to 70 of first chain and residues 120 to 140 of the second chain. Secondly, how can I assign velocities to certain groups? For instance, to r

[gmx-users] stress-strain using pull code

Dear all, I am trying to compute the stress-strain curves, using the pull code explained in Justin’s tutorial. I want to put my crystalline cellulose (which is solvated in water) under tension force at room temperature, and compute the nano-mechanical properties of the system, e.g. Yield modulus

[gmx-users] non-zero total charge

Dear gmx community, I am getting a note before performing the energy minimization step, from grompp that "System has non-zero charge: -0.001135". The system is a crystalline cellulose, built in Amber, using GLYCAM06 force field and the topology and coordinate files have been converted to gromac

Re: [gmx-users] non-zero total charge

ent: vrijdag 30 november 2018 20:28 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] non-zero total charge On 11/29/18 1:13 PM, Ali Khodayari wrote: > Dear gmx community, > > > > I am getting a note before performing the energy minimization step, > from grompp that "Syste

Re: [gmx-users] non-zero total charge

total charge On 11/29/18 1:13 PM, Ali Khodayari wrote: > Dear gmx community, > > > > I am getting a note before performing the energy minimization step, > from grompp that "System has non-zero charge: -0.001135". The system > is a That net charge looks somewha

[gmx-users] Regarding trjconv

Dear all, I am trying to re-center and re-orient an md resulted solute in a box. Yet, I need the box to hold its position and I only need a group of atoms to align along z-direction. Trjconv centers the group in the box but the desired sub-group has a slight inclination which is needed to be or

Re: [gmx-users] Regarding trjconv

: zondag 2 december 2018 17:38 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Regarding trjconv On 12/2/18 11:22 AM, Ali Khodayari wrote: > Dear all, > > > > I am trying to re-center and re-orient an md resulted solute in a box. > Yet, I need the box to hold its position

[gmx-users] Local stress tensors

Dear all, I am trying to extract the local stress tensors for a system undergone a tensile (using the pull code). Can anyone tell me which output (maybe from edr file) can be related to the local stresses? The aim is to achieve the stress-strain curves of crystalline cellulose, in reality. Thank

[gmx-users] regarding editconf

Dear users, I am trying to reorient and re-center my solute using editconf. Performing such I can place the structure at the desired place, yet it is outside the box when I visualize it in VMD. It leads to an error after mdrun complaining about a water molecule not being settled. Here is the

Re: [gmx-users] regarding editconf

ehalf Of Justin Lemkul Sent: dinsdag 15 januari 2019 15:01 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] regarding editconf On 1/15/19 7:46 AM, Ali Khodayari wrote: > Dear users, > > > > I am trying to reorient and re-center my solute using editconf. > Performing such

Re: [gmx-users] regarding editconf

/19 9:34 AM, Ali Khodayari wrote: > Thank you for your response Justin! > I don't really see how it can cause an error, while it might be just a > visualization defect in VMD. > Previously, I tried to perform each step separately, like doing a > centering by -center 0 0 0, but

[gmx-users] turning off non-bonded terms

Dear Users, Does it make sense if I use rcoulomb = 0 and rvdw = 0 in order to turn off non-bonded term calculation during mdrun? If not, is there any recommendations? Thank you for your responses in advanced. Kind regards, Ali -- Gromacs Users mailing list * Please search the archive at htt

Re: [gmx-users] turning off non-bonded terms

Thank you Justin. Kind regards, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: dinsdag 22 januari 2019 15:59 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] turning off non-bonded terms On 1/22/19 9:37 AM, Ali

[gmx-users] Bond breakage modelling

Dear All, We have simulated a cellulose fiber using GLYCAM06 ff parameters converted to GROMACS. The model is validated and works properly. We are investigating the behavior of the material under tensile load. However, as covalent bonds are modelled with a harmonic potential -as it is in mos

Re: [gmx-users] Bond breakage modelling

> dependence on the potential energy also immediately points out an issue > with your cut-off based approach: how will you deal with the angle(s)? > > In literature I have seen some papers of people pulling proteins apart, > breaking cystein bridges. Those may contain some insig

Re: [gmx-users] Bond breakage modelling

effects, use a QM method for the parts that are involved in bond breaking, or use a reactive force field like ReaxFF. Cheers Paul On 2019-02-19 13:35, Ali Khodayari wrote: > Dear Peter, > > Thank you for your prompt reply. > I think I can try the morse potential to see how the system respo

Re: [gmx-users] Bond breakage modelling

ecause there is no influence of the angle on the potential. Peter On 19-02-19 13:35, Ali Khodayari wrote: > Dear Peter, > > Thank you for your prompt reply. > I think I can try the morse potential to see how the system responds. > Could you kindly provide some more info about how t

[gmx-users] Free Energy code

Dear all, I am quite new to free energy calculation, so I apologize if the questions seem naive and of course they are a lot. My intention is to turn off vdw and coulombic interactions to perform some tempering cycles on my system. There are though some questions: 1- I only want to decou

[gmx-users] Defining a new molecule type

Dear Users, I am trying to use the free energy code to partially shut down the non-bonded interactions in part of my system. I only want to decouple interaction in some part of my system, I have put all the desired residues in groups in the index file. What should I indicate for the couple_mol

[gmx-users] regarding solvating a molecule

Dear all, I am trying to solvate a molecule. I am using GLYCAM force field and have generated the *.gro and *.top files through acpype. I want to include tip3p parameter sets from amber99sb.ff. Including the tip3p.itp in the topology file does not suffice as it complains about OW atomtype not foun

[gmx-users] order of atoms in the index file

Hello all, I am trying to calculate the dihedral angels of a group of atoms in a molecule. As I am only interested in part of the molecule, I have manually made an index file containing the desired atoms in groups using gmx make_ndx. Yet, the atom's number in each group is in ascending order. M

[gmx-users] question regarding coulomb potential output

Dear all, I have a question regarding the output of the Coulombic energy from the edr file. I am looking at the interactions between two molecules, and trying to analyse the contribution of different interaction types between these two. Since hydrogen bonds are formed based on the charge dif

[gmx-users] Tabulated potentials

Dear Gromacs users, I’ve got a question regarding the tabulated potentials for bonded interactions. Gromacs recognises and reads the non-bonded potential tables through the energy groups specified. But how can I refer each bond type to its table? I have derived coarse-grained potentials for a c

Re: [gmx-users] Tabulated potentials

Ali Khodayari < ali.khoday...@student.kuleuven.be> wrote: > Dear Gromacs users, > > I’ve got a question regarding the tabulated potentials for bonded > interactions. > > Gromacs recognises and reads the non-bonded potential tables through > the energy groups specifie

Re: [gmx-users] Tabulated potentials

-users] Tabulated potentials Hi, On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari < ali.khoday...@student.kuleuven.be> wrote: > Thank you Alessandra. However, fixing the topology did not remove the > error. It still stands as before: > > A tabulated bond interaction table numb

[gmx-users] Installation on iPad?

Dears, I would like to ask whether it is possible to install GROMACS on iPad as well? Obviously I am not trying to run any simulations on it, but to be able to generate the run files and to transfer them to a cluster. Does it work the same way you’ll have it on any other MacOS? Of course, consi

[gmx-users] Installation on iPad

Dear gmx users, I would like to ask whether it is possible to install GROMACS on iPad as well? Obviously I am not trying to run any simulations on it, but to be able to generate the run files and to transfer them to a cluster. Does it work the same way you'll have it on any other MacOS? Of cour

Re: [gmx-users] Installation on iPad

, at 14:43, Ali Khodayari mailto:ali.khoday...@student.kuleuven.be> > wrote: Dear gmx users, I would like to ask whether it is possible to install GROMACS on iPad as well? Obviously I am not trying to run any simulations on it, but to be able to generate the run files and to transfer the