[gmx-users] protonated histidine with Martini

Dear gromacs users, I want to use Martini force field for my simulation. The simulation is supposed to be performed at acidic environment (pH2.6). In this environment His is protonated. I want to add protonate Hisidine in itp file. Where exactly should I put the charge on S2c or on S3c? Mayb

Re: [gmx-users] minimization problem (Martini simulation)

Thank you very much. It worked. Regina Quoting "Justin A. Lemkul" : pol...@fh.huji.ac.il wrote: Dear Justin, Thank you very much for your answer. Can you please explain me what do you mean by saying "EM wasn't sufficient". What information do you need in order be able to help? I run EM wit

Re: [gmx-users] minimization problem (Martini simulation)

Dear Justin, Thank you very much for your answer. Can you please explain me what do you mean by saying "EM wasn't sufficient". What information do you need in order be able to help? I run EM with emtol=60 and I got the following energies: Steepest Descents converged to Fmax < 60 in 2256 steps P

[gmx-users] minimization problem

Dear Gromacs users and developers, I'm trying to set up simulation. I have a big simulation of something like half million atoms. The problem is that I have a minimization problem. I'm getting the following error: Converged to machine precision, but not to the requested precision Fmax < 10 I

[gmx-users] minimization problem (Martini simulation)

Dear Gromacs users and developers, I forgot to note that I'm talking about a Martini simulation. I'm trying to set up simulation. I have a big simulation of something like half million CG atoms. The problem is that I have a minimization problem. I'm getting the following error: Converged to m

Re: [gmx-users] minimization and simulation problems

Quoting pol...@fh.huji.ac.il: Dear gromacs users, my box dimensions are 368A and when I run the simulation with nsteps=1 it works fine. The mdp files used for minimization and post-em simulation are attached. Thanks again for your help. Regina Quoting chris.ne...@utoronto.ca: What are you

Re: [gmx-users] minimization and simulation problems

my box dimensions are 368A Quoting chris.ne...@utoronto.ca: What are your initial box dimensions prior to em? Also, please copy and paste your .mdp options. Also, what happens when you run the same post-em simulation with nsteps=1 ? -- original message -- Dear all, I'm trying to run sim

[gmx-users] minimization and simulation problems

Dear all, I'm trying to run simulation of 30 proteins in water using the Martini force field. I used water.gro file in order to solvate the proteins. For minimization I used the em.mdp file published at Martini site (http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol par

[gmx-users] Simulation using Martini force field

regarding "parameterization of phosphorylated serine " I checked the Martini papers and I couldn't find how it is done. Can somebody please instruct me. In addition in JCTC paper from 2008 I saw that they simulated pentapeptides without imposing secondary structure. How can I do it? The prob

Re: [gmx-users] Simulation using Martini force field

Thank you very much for you reply. Can you please explain me why do i need secondary structure file at all and why "secondary structure is pre-defined and thus static throughout a simulation"? I didn't see that something like this defined for lipids. How do I use do_dssp to build the needed

[gmx-users] Simulation using Martini force field

Dear Gromacs users and developers, I'm interested to run simulation of natively unstructured protein (casein), that can self assembly and create micelles, using Martini force field. The initial structure of the monomer was created and minimized using Sybyl. This protein includes also 4 phosp

[gmx-users] g_rdf

Dear gromacs users, I want to calculate radial distribution function around my protein. I want to get g_rdf for water molecules (OW) around my protein and g_rdf for COM of some solutes around my protein. The numbers should be averaged over all the frames. I tried to look at the mailing list

[gmx-users] center peptide in simulation box

Dear Gromacs users and developers, I'm trying to visualize .trr from md simulation using VMD. I see that starting from some point (probable as a result of a peptide drift ) my peptide splits and it seems like one part appears at one side of the box and the other on the opposite side. Both par

[gmx-users] simulation settings

Dear Gromacs users and developers, I want to perform simulation of peptide dissolved in water using NPT. For constant temperature I use Berendsen temperature coupling. Do I have to define tc-grps for 2 groups (protein and solvent) or I may use tc-grps =System. What is the difference? The pe

[gmx-users] MD simulation with glycerol

Dear Gromacs users, I'm completely new in Gromacs. I would like to perform a simulation of a peptide in water (SPCE) in glycerol presence using OPLS-AA. I want to know where can I find the parameter and topology file in order to create a solvation box that includes glycerol. Should I constru