[gmx-users] kinetic energy distribution with and without constraints

Hello! I was thinking about the use (or not) of LINCS constraints and v-sites in simulations, and I had a "qualitative" question which I could not understand from reading the papers. It seemed to me that bond stretching and angle bending are atomic motions which would consume energy (though perhaps

Re: [gmx-users] Umbrella Sampling between Nanotubes

Thanks for this! That makes it challenging with a system with more nanotubes then... so I will start with two. Have you ever tried to apply umbrella sampling to caluclate the PMF? Do you think it is the best way? I just want to define the equilibrium distance between two nanotube surfaces... And al

Re: [gmx-users] Bonds/constraits betweeen two moleculetypes?

Thank you! On Mon, Feb 17, 2014 at 1:35 PM, Mark Abraham wrote: > Hi, > > No. The traditional solution is to hack the two moleculetypes together, > which involves some tedious renumbering. A good solution might be found if > someone helps test the code in https://gerrit.gromacs.org/#/c/2566/. >

Re: [gmx-users] Bonds/constraits betweeen two moleculetypes?

I am under impression that pulling code performs this trick. Dr. Vitaly V. Chaban On Mon, Feb 17, 2014 at 2:27 PM, Steven Neumann wrote: > Dear Gmx Users, > > Do you know whether it is possible to apply bonds/distance restraints or > constraints between two atom belonging to different molecule

Re: [gmx-users] Umbrella Sampling between Nanotubes

Not sure that I got your question correctly... The atom indices, which you supply to umbrella code, can be defined as you like, without being bound to the molecules they belong to in the topology files. Therefore, if you need to restraint certain number of atoms in a system, just enumerate them wi

Re: [gmx-users] parameters problem

On 2/17/14, 4:16 AM, Nidhi Katyal wrote: Dear all I am trying to simulate a protein in 3 steps: energy minimization (using em.mdp), position restraints (using pr.mdp) and final production run by NPT ensemble (using full.mdp) at 300K At this temperature, it is known by previous literature surv

Re: [gmx-users] parameters problem

Seems like you're using cut-off electrostatics, which would be a good way of picking lottery numbers, and that's about all. Mark On Mon, Feb 17, 2014 at 10:16 AM, Nidhi Katyal wrote: > Dear all > > I am trying to simulate a protein in 3 steps: energy minimization (using > em.mdp), position rest

Re: [gmx-users] Type of function for bond or bend in SPC/E or TIP3P model

Hi, Those water models are rigid, so the question doesn't really apply. But you can see in their .itp files what they would use if they were flexible, which tends to be the kind of thing you suggested. The bonded function type numbers can be looked up in tables in manual section 5.7, which cross-r

Re: [gmx-users] Bonds/constraits betweeen two moleculetypes?

Hi, No. The traditional solution is to hack the two moleculetypes together, which involves some tedious renumbering. A good solution might be found if someone helps test the code in https://gerrit.gromacs.org/#/c/2566/. Mark On Mon, Feb 17, 2014 at 2:27 PM, Steven Neumann wrote: > Dear Gmx Use

[gmx-users] Bonds/constraits betweeen two moleculetypes?

Dear Gmx Users, Do you know whether it is possible to apply bonds/distance restraints or constraints between two atom belonging to different moleculetypes? Thanks, Steven -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List b

[gmx-users] Type of function for bond or bend in SPC/E or TIP3P model

Dear All, I would like to be sure about the formula for Bond and Angle in itp files, like for SPC/E or TIP3P? Is it like a harmonic form 1/2*K*(R-R0)^2 or K*(R-R0)^2 ? Thanks very much and regards, -- View this message in context: http://gromacs.5086.x6.nabble.com/Type-of-function-for-bond-or

[gmx-users] Type of function for bond or bend in SPC/E or TIP3P model

Dear All, I would like to be sure about the formula for Bond and Angle in itp files, like for SPC/E or TIP3P? Is it like a harmonic form 1/2*K*(R-R0)^2 or K*(R-R0)^2 ? Thanks very much and regards, Leila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Suppo

[gmx-users] parameters problem

Dear all I am trying to simulate a protein in 3 steps: energy minimization (using em.mdp), position restraints (using pr.mdp) and final production run by NPT ensemble (using full.mdp) at 300K At this temperature, it is known by previous literature survey that protein keeps its secondary structure

[gmx-users] Umbrella Sampling between Nanotubes

Dear Gmx Users, I am trying to setup the system of nanotubes with attached polypeptides. I wish to define the equlibrium distance (PMF minima) between them. However in my system, I will have 6 of them in which one is in its quarter in the rectangular each box edge copied across pbc. It is the only