Re: [gmx-users] Neutralizing

Thank you Parham and Justin, Excuse me I have another question, in simulation of a water-peptide system, is it necessary to use QM/MM simulation during the entire process? Because I didn't see it in the tutorials. By the way I generated the pdb file by using charmm-gui then import it in amber

Re: [gmx-users] distance restraints in mdp

Please don't reply to the entire digest. Copy the relevant portions and use a proper subject line. On 3/8/16 8:19 PM, Sana Saeed wrote: dear Justin Lemkuli already run that without restraints, it has no problems. even i used the gro file from the simple 5ns MD but still have these same errors

Re: [gmx-users] distance restraints in mdp

On 3/7/16 10:35 PM, Sana Saeed wrote: i am performing protein ligand binding free energy calculation MD. i have applied distance restraint to 1 pair of atoms. now when i am running md it gives me LINCS warnings. first i thought it is because of wrong geometry so i changed complex, now i am

Re: [gmx-users] Neutralizing

On 3/8/16 3:59 AM, mohammad r wrote: Thank you Parham You mean that it is not necessary to do QM/MM simulation? The trivial task of adding ions to neutralize the net charge on the system certainly does not require anything like QM/MM. -Justin On Tuesday, March 8, 2016 11:13 AM,

Re: [gmx-users] apply force on single molecule

Yes. Take a look at the manual for information on using the Pulling code. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From:

[gmx-users] apply force on single molecule

Dear all, I want look at change in potential energy profile, when i apply force on a molecule on one end where other end fixed in a position. Is it possible do it in gromacs. If yes, how may i proceed? --Masrul -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] unit cell vector warning

Hi, I'm generating the box from the.pdb file with pdb2gmx. The protein in question is 5e1k. I do the simulations in the protein unit cell. Best, Irem > On Mar 8, 2016, at 11:39 AM, Mark Abraham wrote: > > Hi, > > How are you actually generating the coordinate

Re: [gmx-users] unit cell vector warning

Hi, How are you actually generating the coordinate file, and/or the box vectors? As far as I know, nobody's written down the set of vectors that should work sensibly, but it's likely that the gmx tools will write boxes that will definitely work later on... Mark On Tue, Mar 8, 2016 at 4:27 PM

Re: [gmx-users] unit cell vector warning

Hi, An update on the unit cell problem: when I make small changes in the angle, say change 89.45 to 89.00, the error disappears. I’m still getting the same warning. This is with version 5.1.2. Could this be a numerical precision issue (c_y is 0.05, see below) or a bug? I tried to run this

Re: [gmx-users] md of only water - obtaining different pressure in the x , y and z directions

Hi, pressure is an intrinsically macroscopic property (both in size and time), which we may compute for such small systems during such short simulations, but it does not behave ideally under these conditions. Remember that P and V are thermodynamically coupled variables and that liquid

[gmx-users] Pressure of an energy minimized system

Dear all, I have a question regarding computation of pressure of an energy minimized (using steepest decent) system. I would expect that the pressure of an energy minimized system should have contribution only from the virial part of the pressure expression (as there is no temperature). However,

[gmx-users] Extend to Embedding a protein into a lipid box using CGMD

Dear all based on my last question, consider My simulation box file is md.gro and my protein is CG.gro. now if you can, please write the desired command for me to embed this two file and have a lipid bilayer membrane embedded with protein please. best regards

[gmx-users] md of only water - obtaining different pressure in the x , y and z directions

Hi, I am running a simulation which contains only water (using the spc216.gro coordinates and TIP3P model) in an NPT ensemble. I get different values for the average pressure in the x y and z directions. I am running the simulation for up to 10s in a 4nm side cube unit cell. I am using a Nose

[gmx-users] Embedding a protein into a lipid box using CGMD

Dear all during a part of martini tutorial it says: If a stable DPPC membrane with the wanted box dimensions is already available,�genbox�will be able to insert the peptides in the bilayer (the peptides have to be pre-centered and positioned to ensure their presence inside

Re: [gmx-users] Neutralizing

Thank you Parham You mean that it is not necessary to do QM/MM simulation? On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of Biomedical Science) wrote: Dear Sir Use this command: gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral