[gmx-users] water flow

Hi all, I'm trying to explore pressure-induced processes, i.e. externally induced water flow across a porous membrane that spans the entire box in XY. There are obvious choices: 1. Introduce the same type of a membrane without pores and make it a piston with pull code, e.g. constant force or

Re: [gmx-users] Problem in generation of tpr file

To be clear, I did suggest ignoring it _only_ if the warning is: a) understood, b) of known origin, and c) harmless. I am not sure what's your one case is when ignoring warnings is appropriate, but I routinely use '-maxwarn 10,' because I have a bunch of bonded parameters that override default

[gmx-users] Umbrella saming

I do umbrella sampling for different distances of AA perpendicular to nanotube axis. Imagine nanotube is along Y axis and i want to pull AA along just Z axis. But during pulling (i mean most of the time) it trapped in X axis and pulls along x axis. I used pull_vec= 0 0 1 and pull_geometry=

Re: [gmx-users] Doubts in combination rules 2 and 3

Den 2018-06-11 kl. 11:20, skrev Apramita Chand: Please clarify these following doubts regarding combination rules in gromos force field: 1. The ffnonbonded.itp contains c6, c12 terms. If I choose combination rule 1 , it takes V and W as C6 and C12 as given. If combination 2 or 3 are chosen ,

Re: [gmx-users] Doubts in combination rules 2 and 3

On 6/11/18 5:20 AM, Apramita Chand wrote: Please clarify these following doubts regarding combination rules in gromos force field: 1. The ffnonbonded.itp contains c6, c12 terms. If I choose combination rule 1 , it takes V and W as C6 and C12 as given. If combination 2 or 3 are chosen , then

Re: [gmx-users] secondary structure element constraining

On 6/10/18 3:04 AM, alex rayevsky wrote: Dear users! Did anybody meet the problem of positional constraints applied to the secondary structure, namely keeping the 310-helix stable all the time? I've modelled the substructure - a bundle of alpha helices with a 310 helix segment (longer,

[gmx-users] Increase of 5-helix count

Dear gromacs users, I am running a simulation of three alpha helical peptides with a carbon nano tube in a simulation box. Actually I am following a paper and want to reproduce the results. In my simulation every time there is a sudden increase of 5-helix count, means most of the alpha helix

Re: [gmx-users] Rupture force definition

On 6/8/18 2:52 AM, Rakesh Mishra wrote: Dear Justin . I have two query 1-What can be the optimized value of rate can be taken for pulling of dsDNA/dsRNA using gromacs format where solvent is aqua. From your umbrella sampling manual, rate is very high like (0.01 nm/ps), which is equal to

Re: [gmx-users] Problem in generation of tpr file

Please don't respond to the entire digest, and if you're actively asking questions, I suggest changing your list subscription to receive individual emails. On 6/11/18 6:51 AM, Rahma Dahmani wrote: sorry, i am new Gromacs user, where i can find the warning text ? grompp prints very clear

Re: [gmx-users] semiisotropic pressure coupling error

On 6/7/18 5:59 AM, Oguz Gurbulak wrote: Dear Gromacs Users, When I used semiisotropic pressure coupling, I got this error message "Fatal error: The Y-size of the box (4.200315) times the triclinic skew factor (1.00) is smaller than the number of DD cells (3) times the smallest allowed

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 170, Issue 39

sorry, i am new Gromacs user, where i can find the warning text ? 2018-06-11 11:00 GMT+01:00 < gromacs.org_gmx-users-requ...@maillist.sys.kth.se>: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the

[gmx-users] Doubts in combination rules 2 and 3

Please clarify these following doubts regarding combination rules in gromos force field: 1. The ffnonbonded.itp contains c6, c12 terms. If I choose combination rule 1 , it takes V and W as C6 and C12 as given. If combination 2 or 3 are chosen , then are the values converted to sigma and epsilon

Re: [gmx-users] Problem in generation of tpr file

Grompp tells you exactly what to do: "Fatal error: Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors;

[gmx-users] Problem in generation of tpr file

Hi gmx users, I am performing Molecular Dynamic simulations of protein-ligand complex by following steps shown in "GROMACS Tutorials. While moving on to production MD, i coudn't generate the tpr file, in fact i only activated velocity generation parameter in my md.mdp file, and it shows this