[gmx-users] Error in protein insertion in bilipid layer

Dear All, After insertion of my big proteinin lipid bilayer (512) moleules, i used the command : perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat I get a area/ lipid : 10.231 nm2 and on shrinking i get 6. 89nm 2 after only 9 rounds of simulation. But In the tutorial its ar

Re: [gmx-users] Problems with CO2-water simulation

Hi Sujith, Yes, you're right :) Nonetheless, there's nothing intrinsically odd about a positive potential energy. Still, I also think that there will be a considerable portion of carbonate. I think it's good to be suspicious of such reactions in classical simulations. Cheers, Tsjerk On Dec 8, 20

Re: [gmx-users] Problems with CO2-water simulation

Hello Tsjerk, Thanks for the response. I find your argument intuitive. But my simulations are at 30bars and 250K. Isn't the conditions supposed to play a role in making the dissolved state metastable. My system at 250K and 30 bar is like a closed coke can in the refrigerator. I believe there a

Re: [gmx-users] How to scale epsilon parameters of Lennard-Jones term in .top file?

To run REST in gmx using lamda-dynamics, you need to edit both ffnonbonded.itp and ffbonded.itp. In ffnonbonded.itp, you need to define a new atom type corresponding to state B, you need to add something like:; name             bond_type       mass          charge   ptype  sigma  ep

Re: [gmx-users] Problems with CO2-water simulation

Hi Sujith, There is nothing special about positive potential energy. In this case it explains why soft drinks gives bubbles: the CO2 wants to get out. In addition, if it could, it would drive the system to HCO3-/H3O+, which is an energetically more favorable way to store CO2 in water. Cheers, Ts

[gmx-users] Problems with CO2-water simulation

Dear all, I am trying to simulate a water-carbondioxide system at 250K and 30bar. The system consists of 85 CO2 and 1204 water molecules in a 3x3x4 nm box. I used EPM2 and TIP4P potentials for CO2 and water following *Energy Environ. Sci., 2012, 5, 7033-7041* where the authors used

[gmx-users] How to scale epsilon parameters of Lennard-Jones term in .top file?

Hi all, I am trying to run REST in GROMACS following the way proposed by tsuyoshi terakawa. In their method,they implemented REST by rescaling the force-field parameters without even changing the code. I have also searched in the mailing list and found that we can manipulate the scale parameter

Re: [gmx-users] energy groups rerun from reduced xtc file

On Sun, Dec 7, 2014 at 9:54 AM, Harry Mark Greenblatt < harry.greenbl...@weizmann.ac.il> wrote: > BS"D > > Dear Mark, > > Thank you for the advice; removing the checkpoint file does allow > grompp to produce a new tpr file for mdrun. > > In the case, however, where the energy groups were defin

Re: [gmx-users] .itp file of choline molecule

On 12/7/14 3:48 AM, soumadwip ghosh wrote: Dear users, I am studying the dynamics of a double stranded DNA in presence of choline counterion. I am using GROMACS 4.5.6 and CHARMM27 force field for MD simulations. Initially, I made the united atom PDB for Choline using ATB to

Re: [gmx-users] energy groups rerun from reduced xtc file

BS"D Dear Mark, Thank you for the advice; removing the checkpoint file does allow grompp to produce a new tpr file for mdrun. In the case, however, where the energy groups were defined before the run, and so it should be a simple case of rerunning mdrun on CPU's, the use of convert-tpr to

[gmx-users] .itp file of choline molecule

Dear users, I am studying the dynamics of a double stranded DNA in presence of choline counterion. I am using GROMACS 4.5.6 and CHARMM27 force field for MD simulations. Initially, I made the united atom PDB for Choline using ATB topology biliding software. Since the PDB was spec