Re: [gmx-users] proton proton transfer

2010-12-03 Thread Olga Ivchenko
Hi Erik, I think also I can try proton-proton transfer with gromacs later when it will be implemented. best, Olga 2010/12/2 Erik Marklund > Olga Ivchenko skrev 2010-12-02 13.30: > > Dear gromacs users, >> >> I want to simulate proton transfer between water and another small >> molecule in grom

Re: [gmx-users] proton proton transfer

2010-12-02 Thread Erik Marklund
Olga Ivchenko skrev 2010-12-02 13.30: Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I rea

RE: [gmx-users] proton proton transfer

2010-12-02 Thread Ran Friedman
.org [gmx-users-boun...@gromacs.org] On Behalf Of Olga Ivchenko [olga.ivche...@gmail.com] Sent: 02 December 2010 14:59 To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] proton proton transfer Thnaks, Justin. Probably CHARMM is suitable for this. 2010/12/2 Justin A. Lemk

RE: [gmx-users] proton proton transfer

2010-12-02 Thread Ran Friedman
[gmx-users-boun...@gromacs.org] On Behalf Of Olga Ivchenko [olga.ivche...@gmail.com] Sent: 02 December 2010 14:59 To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] proton proton transfer Thnaks, Justin. Probably CHARMM is suitable for this. 2010/12/2 Justin A. Lemkul mailto:

Re: [gmx-users] proton proton transfer

2010-12-02 Thread Olga Ivchenko
Thnaks, Justin. Probably CHARMM is suitable for this. 2010/12/2 Justin A. Lemkul > > > Olga Ivchenko wrote: > >> Dear gromacs users, >> >> I want to simulate proton transfer between water and another small >> molecule in gromacs. In the end I should have the velosity of proton proton >> exchange

Re: [gmx-users] proton proton transfer

2010-12-02 Thread Justin A. Lemkul
Olga Ivchenko wrote: Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrell

[gmx-users] proton proton transfer

2010-12-02 Thread Olga Ivchenko
Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrella sampling, but may be there