Re: [gmx-users] Solvation Free Energy calculation (g_bar)

On 6/18/12 10:41 AM, Daniel wrote: Hi everyone, I'm having problems when calculating Free energy through the g_bar tool. I'm trying to decouple separately the electrostatic and the Vdw terms. So, after performing the mdruns for all Coulombic processes (from 0 to 1, split in 0.1 steps: 0.0-0.1-

[gmx-users] Solvation Free Energy calculation (g_bar)

Hi everyone, I'm having problems when calculating Free energy through the g_bar tool. I'm trying to decouple separately the electrostatic and the Vdw terms. So, after performing the mdruns for all Coulombic processes (from 0 to 1, split in 0.1 steps: 0.0-0.1-0.2...0.9-1.0) and the same for the LJ-

[gmx-users] Solvation Free Energy Calculation

Dear Emanuel: We need you to be much more specific. 1. What link? 2. Even though it might be in the link, you should still provide us with a general protocol that you followed. Chris. -- original message -- I am using Gromacs to calculate solvation of free energy calculation. First I tri

[gmx-users] Solvation Free Energy Calculation

Hi I am using Gromacs to calculate solvation of free energy calculation. First I tried the tutorial I found on the following link and run all the simulations for different lambda values 36 run for both in water and in vacuum and I got 25215.67 is gromacs calculate this in J or KJ? Even if it i

[gmx-users] Solvation free energy

Hi, I want to calculate the solvation free energy of Wild-type human IAPP (hIAPP) with 37 residues in length that residu26 isoleucine is mutated to proline (ile26pro). I used dual topology in Thermodynamic integration (TI) for calculating salvation free energy. For the solvation free energy calcu

Re: [gmx-users] Solvation Free energy using Amber

Ok, thank you for your time. > > > jorge_quint...@ciencias.uis.edu.co wrote: >> Ok Justin, I send You a copy of muy simulation for SFE with two proteins >> + >> water. Look the top file structure. Thanks again. >> > > A quick look at the topologies indicates to me that something is badly > broke

Re: [gmx-users] Solvation Free energy using Amber

jorge_quint...@ciencias.uis.edu.co wrote: Ok Justin, I send You a copy of muy simulation for SFE with two proteins + water. Look the top file structure. Thanks again. A quick look at the topologies indicates to me that something is badly broken. The net charge on each of your protein subu

Re: [gmx-users] Solvation Free energy using Amber

jorge_quint...@ciencias.uis.edu.co wrote: Well, The main reason why I've testedd to obtain solvation free energy (SFE) for toluene is because I want to do it for my future studies related with dimer SFE employing Amber force field with gromacs 4.0. Recently, I've read the tutorial. But, when I

Re: [gmx-users] Solvation Free energy using Amber

Well, The main reason why I've testedd to obtain solvation free energy (SFE) for toluene is because I want to do it for my future studies related with dimer SFE employing Amber force field with gromacs 4.0. Recently, I've read the tutorial. But, when I tried to do the same, I got some errors durin

Re: [gmx-users] Solvation Free energy using Amber

jorge_quint...@ciencias.uis.edu.co wrote: Dear Justin I removed the semicolons but my calculations don't work. The problem is how can I add the other parameters -like bonds, angles and dihedrals- for B-state. I've tried to add it, but I get some problems to obtain the tpr file. Thanks again

Re: [gmx-users] Solvation Free energy using Amber

Dear Justin I removed the semicolons but my calculations don't work. The problem is how can I add the other parameters -like bonds, angles and dihedrals- for B-state. I've tried to add it, but I get some problems to obtain the tpr file. Thanks again. [ bonds ] 1 2 1 --> how can I

Re: [gmx-users] Solvation Free energy using Amber

jorge_quint...@ciencias.uis.edu.co wrote: Dear all. I've tried to calculate solvatin free energy using amber force field and gromacs but unfourtunately I can't include the parameters for B type. Can somebody help me with that, I send you a top file. All of your B-state parameters are comme

[gmx-users] Solvation Free energy using Amber

Dear all. I've tried to calculate solvatin free energy using amber force field and gromacs but unfourtunately I can't include the parameters for B type. Can somebody help me with that, I send you a top file. Best regards, Jorge R. Quintero Grupo de Investigación en Fisicoquímica Teórica y Exp

Re: [gmx-users] Solvation Free energy Calculation

Paolo, As for the LJ decoupling,I cannot obtain a smooth curve and dG/dlambda has large deviations even if I use sc_alpha = 0.5 and sc_power = 1 as suggested by Shirts. This doesn't typically give a smooth curve in the sense of featureless, like the electrostatics curve. However, the particula

[gmx-users] Solvation Free energy Calculation

Dear all, I'm trying to calculate solvation free energy for an ALANINE molecule in water with the usual method: I calculate dG/dlambda for different values of lambda and then integrate. I start with my molecule fully interacting with solvent (water SPC) and then decouple the solute-solvent Coulomb