Re: [gmx-users] UREA + Protein Simulation error.

Dear David, Thanks for the reply, guess i will do some literature survey and see if i can find some validated urea parameters. karan On Mon, Sep 21, 2009 at 8:51 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: karan syal wrote: Dear Justin, Thanks for the reply! I will surely try

[gmx-users] UREA + Protein Simulation error.

Dear Gromacs users, I am trying to run a urea+protein simulation and encountering a few problems at various stages. I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 300K) I am using this equilibrated

Re: [gmx-users] UREA + Protein Simulation error.

karan syal wrote: Dear Gromacs users, I am trying to run a urea+protein simulation and encountering a few problems at various stages. I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 300K) I

Re: [gmx-users] UREA + Protein Simulation error.

Dear Justin, Thanks for the reply! I will surely try minimize the protein in Vacuum and then try adding Urea again. Just that i was wondering how will that effect my artifact bonds which are between Urea and Water, and not at all between any Protein atom and Urea/Sol?? As i mentioned earlier,

Re: [gmx-users] UREA + Protein Simulation error.

karan syal wrote: Dear Justin, Thanks for the reply! I will surely try minimize the protein in Vacuum and then try adding Urea again. Just that i was wondering how will that effect my artifact bonds which are between Urea and Water, and not at all between any Protein atom and Urea/Sol??

Re: [gmx-users] UREA + Protein Simulation error.

karan syal wrote: Dear Justin, Thanks for the reply! I will surely try minimize the protein in Vacuum and then try adding Urea again. Just that i was wondering how will that effect my artifact bonds which are between Urea and Water, and not at all between any Protein atom and Urea/Sol??