Re: [gmx-users] Force constant for umbrella sampling potential

include the 0.5 and I just need to know if this is also the case with gromacs. Thank you. -Dina On 12/17/07 12:34 AM, "Farzad Molani" <[EMAIL PROTECTED]> wrote: > Hi dear > I think it has got 0.5 in equation. > U=0.5*K(r-b)2 > but I dont knoe how do I get K please

[gmx-users] Force constant for umbrella sampling potential

Hello everyone, I would like to know does the harmonic biasing potential for running umbrella sampling in gromacs have a 0.5 in front or is the 0.5 term incorporated into the force constant value that we specify? On other words is the potential V=0.5*k(x-xo)^2 or V=k(x-xo)^2. Thank you in advance

Re: [gmx-users] Pull code with runtype start

Mark, I just checked and it seems I was consulting a manual for an older version than 3.3.1! I guess it was taken out in 3.3.1 Sorry for not being more careful. Thank you. -Dina On 10/20/07 4:16 PM, "Mark Abraham" <[EMAIL PROTECTED]> wrote: > dtmirij wrote: >> I sear

Re: [gmx-users] Pull code with runtype start

19/07 6:55 PM, "Mark Abraham" <[EMAIL PROTECTED]> wrote: > dtmirij wrote: >> Hello everyone, >> >> I just want to clarify if the runtype "start" option works in gromacs-3.3.1. >> I didn't see anything in the mailings list suggesting t

[gmx-users] Pull code with runtype start

Hello everyone, I just want to clarify if the runtype "start" option works in gromacs-3.3.1. I didn't see anything in the mailings list suggesting that it doesn't. If I have runtype = start in my pull.ppa file then gromacs gives me an error:

Re: [gmx-users] ci variable range error in parallel but NOT in serial

-- -Dina On 5/19/07 2:15 PM, "David van der Spoel" <[EMAIL PROTECTED]> wrote: > dtmirij wrote: >> Mark, >> That was a typo in the second paragraph. >> I meant: >> " When I run the exact same system f

[gmx-users] ci variable range error in parallel but NOT in serial

do with the pressure coupling.. Any suggestions -Dina dtmirij wrote: > Hello everyone, > > I am running starting from a minimized/equilibrated structure. > When I run the the system with my serial built executable, it runs fine and > the energies and pressures look fine. > >

[gmx-users] ci variable range error in parallel but NOT in serial

Hello everyone, I am running starting from a minimized/equilibrated structure. When I run the the system with my serial built executable, it runs fine and the energies and pressures look fine. When I run the exact same system from the same starting conditions using my serial built executable on t