[gmx-users] Order parameter

Dear all, I am using GROMACS-4.6.5 for studying gas hydrates and related systems. A useful order parameter which indicates water to hydrate transition is the F4 order parameter where F4 is related to the H--O--O--H dihedral angle for a pair of water molecules. It is found that F4

[gmx-users] F4-Order-parameter

Dear all, I am using GROMACS-4.6.5 for studying gas hydrates and related systems. A useful order parameter which indicates water to hydrate transition is the F4 order parameter where F4 is related to the H--O--O--H dihedral angle for a pair of water molecules Exact expression for F4 can be

Re: [gmx-users] Pdb file

Hello, I guess it is not unusual for gaseous systems to have positive energy. I hope that the Fmax criteria is satisfied. Sujith. On Wed, Aug 12, 2015 at 10:30 AM, Sunil Ghimire ghimiresuni...@gmail.com wrote: I mean potential energy of system (1600 argon atoms) is positive after energy

[gmx-users] Unexpected free energy values.

Dear all, I am studying the CH4-CO2-H2O mixture at low T(270K) and high P (20 bar). Forcefields used: CH4 : Single point LJ site; CO2 : EPM2 (Rigid with two virtual sites); H2O: TIP4P. I computed the free energy of solvation for a CH4 molecule in H2O in the presence of CO2 at different

Re: [gmx-users] Regarding-virtual-sites-tutorial

Hello Justin, Thanks for the mail. I am interested in knowing whether the particle type assigned has any role in the way it is treated by the program. For both virtual sites and the regular atoms, interaction parameters and mass are assigned. So in Gromacs, does the particle type (A or V) has

[gmx-users] Regarding-virtual-sites-tutorial

Dear Justin, I am following your tutorial about CO2 topology using virtual sites. I find that in the topology provided, you have not reassigned the particle type as virtual (V) for the C and O atoms (which are treated as the virtual sites in the model). Instead, they are directly selected from

[gmx-users] About airtual site tutorial

Dear Justin, I am following your tutorial about CO2 topology using virtual sites. I find that in the topology provided, you have not reassigned the particle type as virtual (V) for the C and O atoms (which are treated as the virtual sites in the model). Instead, they are directly selected from

[gmx-users] Location of Bubbles.

Hello, I am observing nucleation and growth of bubbles in a solution of methane in water with methane present at various levels of supersaturation. The system consists of a total 0f 2000 molecules in a cubic box with the number of CH4 varying from 80 to 200. I am using a single point Lennard

Re: [gmx-users] Location of Bubbles.

/6qnoy5o4/strange-behavior-of-water-droplet-on-a-solid-surface-with-verlet-cutoff-scheme-in-gmx-5-0-4 ). Regards, Jan 2015-07-18 8:53 GMT+02:00 sujithkakkat . sujithk...@gmail.com: Hello, I am observing nucleation and growth of bubbles in a solution of methane in water

[gmx-users] Thermostats and MSD

Dear all, I am simulating a system of small hydrophobic solutes ( CH4) dissolved in water. Simulations are performed in the NPT simulation, and I would like to determine the diffusion coefficients from MSD plots. I have two related questions; (1) Is the thermostat going to seriously affect

[gmx-users] Question on forcefields?

Dear all, Is it possible that a model for a simple molecule (say CO2) which can accurately predict macroscopic properties (like density), but still can have error in the microscopic behavior, like diffusivity or the pair interaction functions ? Please share your thoughts. Regards, Sujith.

Re: [gmx-users] Virtual sites and diffusion coefficients.

are you able to reproduce the original parametrization results? Mark On Tue, Feb 3, 2015 at 8:04 AM, sujithkakkat . sujithk...@gmail.com wrote: Dear all, I tried simulating the CO2-water mixture with CO2 at a low concentration (0.003 mole fraction) at various temperatures at 1 atmos

[gmx-users] Questions about CO2.

Dear all, I went through the mails about the use of virtual sites for representing linear molecules like CO2. I also read that GROMACS cannot handle angle bending potentials at 180 degrees in an appropriate manner. My system consists of EPM2-CO2 dissollved in TIP4- H2O. I

Re: [gmx-users] PMF and RDF

for some distances however. Erik Kind regards, Erik On 9 Dec 2014, at 06:39, sujithkakkat . sujithk...@gmail.com wrote: Dear all, I read in *Phys. Chem. Chem. Phys., 2009, 11, 10427-10437*, that the radial distribution function is directly related to Potential of mean

[gmx-users] PMF and RDF

Dear all, I read in *Phys. Chem. Chem. Phys., 2009, 11, 10427-10437*, that the radial distribution function is directly related to Potential of mean force through RDF=exp(-PMF/kT). My question is why would someone worry about computing PMF in a simple case like interaction between two

[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

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

, if it could, it would drive the system to HCO3-/H3O+, which is an energetically more favorable way to store CO2 in water. Cheers, Tsjerk On Dec 8, 2014 6:50 AM, sujithkakkat . sujithk...@gmail.com wrote: Dear all, I am trying to simulate a water-carbondioxide system at 250K

[gmx-users] question about modified LJ combination rule

Dear all, I am studying a water-methane system with tip4p-Ice for water and oplsaa for methane. What I want to try is modify the intermolecular non-bonded interaction between methane and water. I just want to multiply the combination rule (geometric mean) used to obtain the mean well depth

[gmx-users] RDF of solvation shell molecules

Hello, I would like to know if it is possible to plot the RDF of water molecules belonging to the solvation shell of a solute. I mean, I want to know the effect of the solute on the water arrangement in the solvation shell. Is there a way to do this? Regards, Sujith. -- Gromacs Users

Re: [gmx-users] RDF of solvation shell molecules

On Thu, May 22, 2014 at 8:18 PM, sujithkakkat . sujithk...@gmail.com wrote: Hello, I would like to know if it is possible to plot the RDF of water molecules belonging to the solvation shell of a solute. I mean, I want to know the effect of the solute on the water arrangement

Re: [gmx-users] High density after genbox

On Tue, May 20, 2014 at 12:50 PM, sujithkakkat . sujithk...@gmail.com wrote: Hello, I am working on a water-methane system with OPLSAA for methane and TIP4P/Ice for water. What I find strange is that after solvating the methane molecule with water (tip4p/ice) using the genbox

[gmx-users] High density after genbox

Hello, I am working on a water-methane system with OPLSAA for methane and TIP4P/Ice for water. What I find strange is that after solvating the methane molecule with water (tip4p/ice) using the genbox routine, the density appears to be very high at 1661.04 (g/l) . The number of water molecules

Re: [gmx-users] Positive energy .

at 8:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/14/14, 12:39 AM, sujithkakkat . wrote: Hello Justin and others, Thank you for the response . Here are mode details of the system; ( in the order ; MDP settings, itp and top files) . The system consists of 460 water molecules and 1

[gmx-users] Positive energy .

Dear all, I am running simulations for a water-CO2 system using the OPLSAA forcefield, where I use TIP4P/Ice water model and the EPM2 model for CO2. After energy minimization I found the value of potential energy to be positive, and also the maximum force value was high (I requested Fmax 10

Re: [gmx-users] Positive energy .

Hello Justin and others, Thank you for the response . Here are mode details of the system; ( in the order ; MDP settings, itp and top files) . The system consists of 460 water molecules and 1 CO2 molecule . I am trying to find the free energy of solvation for CO2 in water at various

[gmx-users] About cutoffs for OPLSAA

Dear all, I want to study a system consisting of water, methane and CO2. I will use TIP4P/Ice , OPLSAA and EPM2 models respectively for the components . My problem is, how do I make a choice of the cutoff lengths, for a system which uses different molecular models which were

[gmx-users] about tutorial on virtual sites

Hello Justin, I found that in the virtual sites section of your tutorial, the energy values of the system large positive . You had warned in the topology file that the choice of the partial charges used are not guaranteed to work always with OPLSAA . However, the momentum of inertial values

[gmx-users] Reproducibility in free energy calculations.

Hello Justin, I tried the free energy calculations in your tutorial at different sets of conditions. Also I repeated a simulation at the same conditions with same parameters, thrice on the same computer on same number of processors. The results in the three cases where different (4.16 +/- 0.19

Re: [gmx-users] Dubious results with NPT

constraint_algorithm= LINCS continuation= no lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 Regards, Sujith. On Wed, Mar 12, 2014 at 5:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/12/14, 7:51 AM, sujithkakkat . wrote

Re: [gmx-users] Dubious results with NPT

be that you've appended to a previous 5ns trajectory, not run a new trajectory. Check the .log file and the length of time you expected this job to run (wall and simulation). Mark On Fri, Mar 14, 2014 at 9:02 AM, sujithkakkat . sujithk...@gmail.com wrote: Hello, This time I tried

Re: [gmx-users] Dubious results with NPT

Hello, After a while I got back to the problem posted here. This issue was the large value for average pressure(~25 bar against the reference pressure of 1 bar) in NPT simulations with parrinello rahman barostat. The system studied is cyclohexane-water system with an interface. The forcefield

[gmx-users] A question about blowing up

Hello, I am following justin lemkul's tutorials for the cyclohexane-water biphasic system using Gromos96 forcefield. Things went well till NVT equilibration where I had this Blowing up issue. Shortening the time step alone did not help, and it was difficult for me to figure out what was

[gmx-users] Severe error with NPT

Dear GROMACS users, I am new to GROMACS, and recently started using the version 4.6.5. I have seen a lot of NPT related issues raised earlier in this forum, but in my case the error looks much more severe. I am following Justin Lemkul's tutorial (

Re: [gmx-users] Dubious results with NPT

Hello, Thank you both for the comments. I am using gromos96 forcefield . I read a little bit and as you said the nonbonded cutoff has to be higher. The tau_p=5ps was chosen , since the manual mentions that the value has to be raised by 4-5 times on going from berendsen to parrinello-rahman