Re: [gmx-users] Shift functions

2012-02-11 Thread Elisabeth
On 10 February 2012 09:41, Mark Abraham wrote: > On 11/02/2012 1:19 AM, Elisabeth wrote: > > > Hello all, >> >> Does the shift function use group based truncation? >> >> >> See the discussion of charge groups in manual section 3.4.2. >> > > Thanks Mark. > > -1- First of all if I am right cha

Re: [gmx-users] Shift functions

2012-02-10 Thread Mark Abraham
On 11/02/2012 1:19 AM, Elisabeth wrote: Hello all, Does the shift function use group based truncation? See the discussion of charge groups in manual section 3.4.2. Thanks Mark. -1- First of all if I am right charge groups in gromacs language in identical to "group based trun

Re: [gmx-users] Shift functions

2012-02-10 Thread Elisabeth
> Hello all, > > Does the shift function use group based truncation? > > > See the discussion of charge groups in manual section 3.4.2. > Thanks Mark. -1- First of all if I am right charge groups in gromacs language in identical to "group based truncations"? Manual 342: "This reduces the cut-o

Re: [gmx-users] Shift functions

2012-02-10 Thread aldi asmadi
Hi Elisabeth, You could check the following paper: D. van der Spoel and P. J. van Maaren. The origin of layer structure artifacts in simulations of liquid water. J. Chem. Theory Comput., 2:1, 2006. Aldi On Fri, Feb 10, 2012 at 4:58 PM, Mark Abraham wrote: > On 11/02/2012 12:52 AM, Elisabeth wro

Re: [gmx-users] Shift functions

2012-02-10 Thread Mark Abraham
On 11/02/2012 12:52 AM, Elisabeth wrote: Hello all, Does the shift function use group based truncation? See the discussion of charge groups in manual section 3.4.2. In the manual I see: by using shifted forces there is no need for charge groups (=group based?!) in the neighbor list? Can an

[gmx-users] Shift functions

2012-02-10 Thread Elisabeth
Hello all, Does the shift function use group based truncation? In the manual I see: by using shifted forces there is no need for charge groups (=group based?!) in the neighbor list? Can anyone shed some light on calculation of shifted forces? Thanks, Eli -- gmx-users mailing listgmx-users@g

[gmx-users] shift functions in gromacs

2011-07-23 Thread Павел Кудрявцев
Hello everyone, I'd like to ask for some clarification of actual form of shift fuctions used in gromacs. Due to gromacs tutorial 4.5.4 (section 4.1.5) and equations 4.23, 4.26-4.31 shift fuction seems to depend only on 2 user-defined conctants - r1 and rc which seems to be rvdw_switch and rvdw res