[gmx-users] About free enrgy calculation

Thank you for your previous reply Sorry  In previous Mail i wrongly  stated that decoupling CNT ( as you stated  it is big  Molecule ) To do free energy calculation based on on your tutorial 6( methane/water)   I  want to decouple  Water  from CNT which is Wrapped by  assembly of Cyclic

[gmx-users] MD for extracellular and transmembrane system

Dear all Gromacs user, I am knew to Gromacs for molecular dynamics. One off the hurdle I encountered is that can I use GROMACS for modelling protein with extracellular and transmembrane domain i.e., maintain water/lipid system in molecular dynamics simulation. Can I add the water system

[gmx-users] g_dielectric errors for getting frequency dependent dielectric constants

Dear all, I have some questions when calculating frequency dependent dielectric constants throughg_dielectric. 1. After using g_dipoles -corr mol command to get the dipcorr.xvg, if I uesd g_dielectric program, the error is as following. Fatal error: nparm = 0

Re: [gmx-users] About free enrgy calculation

On 6/1/14, 3:30 AM, vidhya sankar wrote: Thank you for your previous reply Sorry In previous Mail i wrongly stated that decoupling CNT ( as you stated it is big Molecule ) To do free energy calculation based on on your tutorial 6( methane/water) I want to decouple Water from CNT

Re: [gmx-users] MD for extracellular and transmembrane system

On 6/1/14, 3:51 AM, rahul dhakne wrote: Dear all Gromacs user, I am knew to Gromacs for molecular dynamics. One off the hurdle I encountered is that can I use GROMACS for modelling protein with extracellular and transmembrane domain i.e., maintain water/lipid system in molecular

[gmx-users] help needed

Dear All, I am testing my gromacs code using user-specified potential functions (LJ as well as Buckingham as non-bonded potentials). *Minimization run with these potentials runs fine*. However, equilibration run gives following error at which I am clueless. Could anyone help? Is it because total

Re: [gmx-users] help needed

More information: As the log file shows, coulomb interaction energy is shooting to nan during equilibration where error occurs. Coulomb interaction energy during minimization is finite. Thanks Chetan On Sun, Jun 1, 2014 at 4:44 PM, Chetan Mahajan chetanv...@gmail.com wrote: Dear All, I am

Re: [gmx-users] help needed

Hi, What's the smallest relevant neutral system you can think of? Test your implementation of your model on that, on a local machine, not a supercomputer ;-) If there's any diagnosis of why the crash happens, it will be in the log file. But you seem like you have far too many variables to know

[gmx-users] hydrogen bond analysis

Dear all I wish to analyze hydrogen bonds in a gromacs MD trajectories with g_hbond. I want to get information about the life time of individual hbonds between the receptor and ligand in the structure through the trajector. in the output log file of g_hbond command, I can find the list of

[gmx-users] Simplified picture: comments invited

Hi, Unfortunately, there is no scope I can try smaller version of the system. However, let me explain one lead that I indicated earlier. Coulomb energy at the end of minimization is -5E-7, which becomes -nan at the zeroth step of NPT molecular dynamics run after minimization and thus code

Re: [gmx-users] Why does the list keep unsubscribing me?

Hi Administrators, I have been unsubscribed now for the third time (twice in the same month). This is getting increasingly annoying now. Can there be a fix to mailman to look for genuine email, or to send a confirmation link to unsubscribe (the same as for subscription) ? Thanks, Abhi

[gmx-users] Soln to visualised long molecule bonds across box in VMD

When visualising a simulation with VMD, a significant number of people encounter an issue where the bonds, typically appearing when loading a trajectory on a starting structure (in which the bonds are correct), then being drawn across the box. There are some extensive discussions on this