[gmx-users] infinite molecule problem

Dear gmx users, I want to simulate the solid/liquid interface, so I build an infinite inorganic molecule with pbc=full first. After I ran the system with vaccum (at the top of system) for a few ps, I found the crystal oscillating along the xy plane collectively and frequently, so there were too

[gmx-users] Double or single precision

Hi, can anybody explain me the different uses for the single and the double precison packages. Are there situations that explicitly require a double precision package, and situations when i can use a single precision? Thanks a lot Jacopo ___ gmx-users

[gmx-users] Re: Re: RMSD VS. parallel simulation (Mark Abraham)

gmx-users-request,您好！ Message: 1 Date: Sat, 5 Apr 2008 11:48:15 +0800 From: DeChang Li [EMAIL PROTECTED] Subject: [gmx-users] RMSD VS. parallel simulation To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Dear all, I

[gmx-users] about tip3p water model

Dear all, Can I use TIP3P model with Gromacs force field? Moreover£¬why there isn't tip3p.gro in top file? Thank you in advance! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] How to specify conection between 2 molecule in the top file?

Frankie Montenegro wrote: Hi everyone, I have a question regarding a forcefield build. Is there a way to specify in the topology file how to bond two molecules one to another? The GROMACS implementation of bonded interactions doesn't permit them between atoms in different [ molecules ]

Re: [gmx-users] about tip3p water model

Quoting Rui Li [EMAIL PROTECTED]: Dear all, Can I use TIP3P model with Gromacs force field? First, it has been stated many times over that ffgmx is deprecated and is questionable at best for use in new production simulations. There was a discussion across the list about this not too long ago.

[gmx-users] infinite molecule problem - Follow up info

Dear gmx users, My previous question are: I want to simulate the solid/liquid interface, so I build an infinite inorganic molecule with pbc=full first. After I ran the system with vaccum (at the top of system) for a few ps, I found the crystal oscillating along the xy plane collectively and

Re: [gmx-users] How to specify conection between 2 molecule in the top file?

Dear Mark, I can most certainly express myself in an exteremely dry and stuffed up manner if it is more to your liking. It seems that my previous 20 postings weren't critized at all ,even though my posts were utterly incomprohensible and my english apolling. But I promiss to do my absolut best

Re: [gmx-users] How to specify conection between 2 molecule in the top file?

Frankie Montenegro wrote: Would you be kind to clearify the second part of may question? Namely, could + and - signs, mentioned in the manual and used in the rtp files be helpfull to me in this case? They allow you to create bonded interactions between atoms belonging to different parts

[gmx-users] how to control temperature

Hi all, I want the temperature is gradually increased by heating from 0 to 300 K for the first 20 ps, and then it is kept at 300 K for the next 100ps.How can I do this in gromacs? Thanks in advance! ___ gmx-users mailing list

Re: Re: Re: [gmx-users] NVT and NVE

Hi Markus, It means that I should change cutoff to the Shift, right (manual 7.3.10) jes On Sat, 05 Apr 2008 Markus Miettinen wrote : Hi Jes, to me it seems that you have rlist = rvdw: nstlist = 10 rlist= 1.0 rvdw = 1.0 This

Re: [gmx-users] how to control temperature

You can do this with simulated annealing which is implemented in gromacs. See the simulated annealing section in the manual. Cheers Mitch Rui Li wrote: Hi all, I want the temperature is gradually increased by heating from 0 to 300 K for the first 20 ps, and then it is kept at 300 K for the