Re: [gmx-users] Free Energy Calculations: Error during minimization step.

Hello Wes, I ran some more test simulations. I think the error is because I added counterions to neutralize my system (it has a +2 charge) prior to the free energy. Without the counterions, the simulations are running fine. Though, I don't know whether such a behavior is expected. Such a setup

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

On Tue, Sep 12, 2017 at 12:17 AM, Abhishek Acharya wrote: > Just to add to the above post, running a none to vdw-q tranformation using > the following parameters also results in the same error for simulation at > first lambda. > Do you get this error on a normal

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

Just to add to the above post, running a none to vdw-q tranformation using the following parameters also results in the same error for simulation at first lambda.

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

Hello GROMACS users, As Wes had advised previously in this thread, the issue with the vdw tranformations was rectified by removing the charges from the topology file. Thereafter, I also tried running free energy calculations using the following free-energy parameters:

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

You can do them separately, but the charges need to have been turned off for the molecule you are transforming for the second step when turning off vdw. In other words, all charges must be 0.0 for the molecule in the topology file for the vdw transformation. Is that what you've done? Justin's

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

On Sat, Sep 9, 2017 at 10:10 AM, Abhishek Acharya wrote: > Hello Wes, > > Thanks for your reply. > > Sorry, I did not understand why we need to turn off charges first and then > vdw, if the are performing both steps separately. > > I was attempting to perform the vdw

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

Hello Wes, Thanks for your reply. Sorry, I did not understand why we need to turn off charges first and then vdw, if the are performing both steps separately. I was attempting to perform the vdw and charge transformations separately. So for the vdw transformation, if I use c-lambda0=vdw and

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

On Sat, Sep 9, 2017 at 2:09 AM, Abhishek Acharya wrote: > Dear GROMACS users, > > I am trying to estimate the free energy of solvation for a ion. But, I am > facing a problem while running simulations for the deltaG_LJ calculation. > The simulation at vdw_lambda=1.0

[gmx-users] Free Energy Calculations: Error during minimization step.

Dear GROMACS users, I am trying to estimate the free energy of solvation for a ion. But, I am facing a problem while running simulations for the deltaG_LJ calculation. The simulation at vdw_lambda=1.0 crashes during the steepest-descent minimization step, with the following error.