Re: Re: [gmx-users] Recommended parameters for NVE simulation of SPCE water

2011-08-17 Thread wibke . sudholt
Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, August 22, 2011. For all questions about CloudBroker and the CloudBroker Platfor

Re: [gmx-users] Recommended parameters for NVE simulation of SPCE water

2011-08-17 Thread Michael Shirts
Hmm. Even now, I'm noticing problems with what I sent: It should be; > rcoulomb                    = 1.3. For PME, rlist should equal rcoul. PME-switch can improve energy conservation, but the wrong PME-switch parameters can affect the results too much. PME w/o switch should be appropriate fo

Re: [gmx-users] Recommended parameters for NVE simulation of SPCE water

2011-08-10 Thread Michael Shirts
> 1.  NOTE 1 above suggests that I use vdwtype = Shift.  When I do this, do > you recommend that I apply long range dispersion corrections for both energy > and pressure, using DispCorr = EnerPres, or for only energy, using DispCorr > = Ener?  Typically, for various (non-NVE) calculations, I have b

Re: [gmx-users] Recommended parameters for NVE simulation of SPCE water

2011-07-13 Thread Justin A. Lemkul
Andrew DeYoung wrote: Hi, I am a Gromacs novice and am trying to simulate 1000 SPC/E water molecules (with the usual charges) in the NVE ensemble. I am trying to obtain good energy conservation. My configuration contains a 10-by-10-by-10 cubic crystal of SPC/E waters, with a lattice constan