[gmx-users] Re: Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

2012-11-01 Thread Emma Eriksson
displays, at least that is what can be concluded from version 4.0. Could someone please help me to figure this out? Thanks. Emma > On 2012-10-08 09:05, Emma Eriksson wrote: > Thank you David for your response. Please see my reply below. > > On 2012-10-04 11:50, Emma Eriksson wrote:

[gmx-users] Re: Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

2012-10-09 Thread Emma Eriksson
On 2012-10-08 09:05, Emma Eriksson wrote: > Thank you David for your response. Please see my reply below. > > On 2012-10-04 11:50, Emma Eriksson wrote: >> Dear all, >> >> I am using the pull code in Gromacs 4.5.5 to constrain the distance in one >> direction (

[gmx-users] Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

2012-10-08 Thread Emma Eriksson
Thank you David for your response. Please see my reply below. On 2012-10-04 11:50, Emma Eriksson wrote: > Dear all, > > I am using the pull code in Gromacs 4.5.5 to constrain the distance in one > direction (z) between a small molecule and a lipid bilayer. I run separate > s

[gmx-users] Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

2012-10-04 Thread Emma Eriksson
Dear all, I am using the pull code in Gromacs 4.5.5 to constrain the distance in one direction (z) between a small molecule and a lipid bilayer. I run separate simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder. The pull parameters are the following: pull

[gmx-users] Pull code problem: Large fluctuations in pull force in Gromacs 4.5.1 compared to 4.0.5

2012-01-12 Thread Emma Eriksson
Dear all, I have a problem using the pull code in Gromacs 4.5.1. I am running simulations with a small molecule at constrained distances from the bilayer center in a membrane (z-direction) in order to calculate permeability data. I use the force acting on the molecule (pullf.xvg) at different di