Re: [gmx-users] system is exploding

Quoting Baofu Qiao : > > If you are really sure about the topology, the problem is the initial > structure. Try to use PackMol to build it. > For simple molecules in water, there is no need for a complicated program like packmol. Such a configuration can easily be built in Gromacs. I have yet t

Re: [gmx-users] system is exploding

check your custom topology (this is where the error is 99% of the time), use qm minimized starting structures, make sure your structure matches your topology (atom names,numbers,ordering, etc.), test single molecules in vacuum first and/or reduce the step size of your SD minimizer. On 11/26/20

Re: [gmx-users] system is exploding

If you are really sure about the topology, the problem is the initial structure. Try to use PackMol to build it. On 11/26/2010 11:42 AM, Olga Ivchenko wrote: > I tried today to run minimization in vacuum for my small molecules. This has > the same error. > > 2010/11/26 Baofu Qiao > > >> Have

Re: [gmx-users] system is exploding

I tried today to run minimization in vacuum for my small molecules. This has the same error. 2010/11/26 Baofu Qiao > > Have you run the energy minimization (or further simulation to optimize > the structure and test the FF) on the small molecule before you added it > into water? > > On 11/26/201

Re: [gmx-users] system is exploding

Have you run the energy minimization (or further simulation to optimize the structure and test the FF) on the small molecule before you added it into water? On 11/26/2010 11:26 AM, Olga Ivchenko wrote: > Dear gromacs users, > > I am trying to run simulations for small molecules in water. Topology

[gmx-users] system is exploding

Dear gromacs users, I am trying to run simulations for small molecules in water. Topology files I created by my self for charm ff. When I am trying to start energy minimization I got an error: Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps = 1000 That's means my system is

Re: [gmx-users] System is exploding

abhigna polavarapu wrote: I am running a 10ns simulation on a 42 mer peptide. I am doing this for predicting the stability of the beta sheet. So I deleted a bond called the lactame bond between two amino acids Lys and Asp. So if I just create mutation at any other position in the beta sheet th

[gmx-users] System is exploding

I am running a 10ns simulation on a 42 mer peptide. I am doing this for predicting the stability of the beta sheet. So I deleted a bond called the lactame bond between two amino acids Lys and Asp. So if I just create mutation at any other position in the beta sheet the mdrun crashes with an error

Re: [gmx-users] system is exploding!!!!!

Hi, Please avoid the use of multiple exclamation marks or capitals in subjects. The problem may be of tremendous significance to you, but your urgency means very little to the others of us, and you will get more helpful feedback if you sound like you are describing your symptoms calmly and clearly

[gmx-users] system is exploding!!!!!

Hello Gmx users I have recently upgraded to gromacs3.3. I was running an MD simulation of a protein-ion complex immersed in water, on gromacs3.2 before and it worked fine. Later I rerun the same simulation on gromacs 3.3 but with different starting velocity. I am getting this error now: Warning: