[gmx-users] water model and force field

Dear gmx-users, Am doing a simulation of DPPC bilayer with a polymer. I read from various papers that SPC is the best water model for lipids and GROMOS 87 is the best force field adapted for the lipids. So i made use of SPC and gromos 87 in my simulation .But am not clear with GROMOS 87 file for

[gmx-users] Timestep and force field

Dear gmx user, Am a beginner to gromacs,I have a few questions to be clarified before getting started with gromacs. 1.on giving pdb2gmx gromacs offers force fields fom 0 to 6 and also i read like opls-aa is the best forcefield for protein? why is that so?What kind of forcefield do i have to choo

[gmx-users] Timestep and force field

Dear gmx user, Am a beginner to gromacs,I have a few questions to be clarified before getting started with gromacs. 1.on giving pdb2gmx gromacs offers force fields fom 0 to 6 and also i read like opls-aa is the best forcefield for protein? why is that so?What kind of forcefield do i have to choo

[gmx-users] Atom H2 not found in rtp

Hello, gmx-users， i used command"pdb2gmx -f a.pdb -ignh" but i got error like: Fatal error: Atom H2 not found in rtp database in residue BEN --- there are no H2 atom in my file. why? my version is gromacs3.3.3 -varsha

[gmx-users] make_hole

Dear all, When i look into the gromacs contributions couldnt locate mdrun_make_hole.tar.gz ..Is this a seperate file or is it coming with gromacs 3.14 only?it will be helpful if somebody send me a link to download mdrun_make_hole.tar.gz? -varsha ___ gmx

[gmx-users] Insertion of polymer into the bilayer

Dear all, I want to insert polymer in the aqueous phase of the bilayer.when i read through the mailing list i found that this can be done in three ways 1.By using genbox command genbox -cp polymer.pdb -cs bilayer.pdb -o merged.pdb this results in the insertion of polymer molecules to the centre

[gmx-users] mdrun halting

Dear all, The production run of DPPC bilayer with 128 lipids and 3655 water and some solvent molecules is halting without completion.As justin suggested ,i changed the columb type from cut-off to PME.It keeps on running for hours together.The system is well equilibriated and i found no issues or w

[gmx-users] Insertion of polymer into bilayer

Dear all, Thanks for all your valuble suggestion in helping me to build polymer.I sucessfully built the polymer and its working fine without any issue. Now my next step is to insert the polymer in aqueous phase of a lipid bilayer.How can i do that with gromacs?,since am a new user to gromacs,pleas

[gmx-users] .mdp file for polymer

Hello sir, On giving gmxdump its giving me an error saying "segmentation fault.My box size is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5 timesteps and with columb type=PME. I read from mailing list that PME calculations requires large amount of memory space.Is this an issue with dime

[gmx-users] .mdp file for polymer

hello sir, I made nstvout and nstfout parameters to zero and frequency to update position coordinates alone (nstxout) to 1000.But still am getting only one frame when viewed the trajectory in VMD.It is an NVT ensemble.How can i get more than one frame?I think the timestep and nsteps i have giv

[gmx-users] Number of Frames in Trajectory

Dear users, Am trying to simulate a polymer in vaccum.But when i make the production run and view trajectory(.trr) files in VMD am getting only one frame.Here's a part of my mdp file: title = polymer cpp = /lib/cpp constraints = all-bonds integrator

[gmx-users] Rtp for polymer.

Hello justin, Am sorry to say that its not useful.But what i mean is that the rtp constructed manually is building up the polymer and generating topology files and gro files. But when i look into the gro file with vmd the connectivity between each of the monomer is not built.That is my polymer co

[gmx-users] constructing polymer.itp files from monomer files obtained from prodrg server

Dear all, Am trying for a simulation with polymers on a lipid bilayer.when i give the entire polymer file which consists of 228 atoms to prodrg server for generating itp files its taking only a block of polymer as input and generating itp files for that polymer alone.I have two different monomer

[gmx-users] "No default proper Dih.type

Dear all, Am trying to do simulation of DPPC membrane.Am using ffgmx force field,because other force fields doesnt have DPP residue,so got an error saying "Residue DPP not in topology database. So i generated topology file using pdb2gmx -ff gmx -f inp.pdb -o out.gro now after few more steps i up

[gmx-users] How to get topol.top files from DRGGMX.ITP files?

Dear all, Am using Dundee prodrug server for the simulation of polymers..I have generated DRGGMX.ITP files for running gromacs simulation.How to get a topology file with .top extension so that i can use it in the grompp step from this. I used x2top command to generate topolgy file with DRGFIN.GR

[gmx-users] Tcl script

I just now started with TCL scripting.And it will be helpful if someone tell me how to write a TCL script for the following queries.? Given a ubiquitin protein , 1.what is the end-to-end distance ( c-terminal and N-termnal) distance of ubq and how does it change with time? 2. what is the total c