[gmx-users] RE: Potential bug? Different results from different versions of gromacs with cos_acceleration

Just a follow up on this problem. I think it is known that there is some bug in the 1/viscosity calculation in Gromacs version of 4.5.3. As shown in the following posts in the mailing list:1. lists.gromacs.org/pepermail/gmx-users/2011-January/057596.html2. lists.gromacs.org/pepermail/gmx-users/

[gmx-users] Potential bug? Different results from different versions of gromacs with cos_acceleration

Dear Gromacs users and developers, I found Gromacs 4.5.5 problematic in NEMD calculations for viscosity. As a simple benchmark, I did some calculations for water (TIP5P) and the results are confusing. I applied two methods for the calculation in 300K, 512 waters: 1. momentum fluctuations, 2. pe

Re: [gmx-users] PR

Thank you for the discussion. I am basically having a similar problem: position restraining (PR) 2 plates in NPT and the system blow up (posted here: http://lists.gromacs.org/pipermail/gmx-users/2010-November/055975.html). I will try to use smaller time step to see whether the situation becomes be

Re: [gmx-users] question regarding to PMF calculation between 2 plates

Hi Chris, Thank you so much for the idea! It is a good idea of using umbrella sampling technique. But I am not sure whether it is just a matter of averaging 3 PMFs as the final result. To be physical, we need the 2 plates to be parallel to each other at any time, right? With 3 pull groups (or mor

[gmx-users] question regarding to PMF calculation between 2 plates

Dear GROMACS users, I have a question for calculating the potential of mean force between 2 plates (i.g., graphene) in water. It is not technically as simple as it seem. I found this question has been asked many times (I sum them up in the bottom of this note, so maybe it will be helpful for someo

Re: [gmx-users] Two Types of van de Waals interactions in one system

this table as your tabulated potential, the total energy should be conserve in NVE. Thanks, Zhe On Tue, Dec 8, 2009 at 2:32 PM, David van der Spoel wrote: > Zhe Wu wrote: >> >> Dear David, >> >> Thank you so much for your reply! I did try to use nstlist = -1 and I >&

Re: [gmx-users] Two Types of van de Waals interactions in one system

be table.xvg.) So it seems to me there is no explicit way I can use shift function. Or should I shift the function by changing the potential in the table? Thanks again for your help. Zhe On Tue, Dec 8, 2009 at 1:38 PM, David van der Spoel wrote: > Zhe Wu wrote: >> >> I agree w

Re: [gmx-users] Two Types of van de Waals interactions in one system

I agree with that. But I don't know why, when using tabulated potential, I cannot even get a box of LJ particles to have energy conservation in NVE. Anyone has some idea? Zhe On Tue, Dec 8, 2009 at 3:52 AM, XAvier Periole wrote: > > One solution would be to use tabulated potential for which the

[gmx-users] energy conservation with lookup table

Dear GROMACS developers and users, I observed a problem with energy conservation in NVE simulation with nonbond potential lookup table. I use the same setup for the L-J particles, one in the "analytical" way in the *.itp file as functional form 1 (with vdw_type= switch), the other using User defin