[gmx-users] Re: Constraints not working in pull code (sometimes, sometimes not)

Dear all, I have reported a week ago update about my troubles with octanol/water slab and pulling simulations, where COM code starts to report a wrong distances between centre-of-masses between two groups when bigger box (see bellow) is used. So far, smaller box cured our actual calculation probl

[gmx-users] Re: Constraints not working in pull code (sometimes, sometimes not)

Dear all, We have tested more strange behavior of constraints from pull code for calculation of free energy differences small molecule on DOPC membrane and octanol slab. As I have reported previously, while the errors in free energy differences on DOPC were rather small, the errors on octanol were

[gmx-users] Re: Constraints not working in pull code (sometimes, sometimes not)

Dear Justin Thank you for your responses, but it still is not clear to me why is that happening > I don't see any real problem here. The DOPC membrane probably holds its shape > better than the octanol slab and thus the reference position (which determines > the constraint) is less mobile. That

[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

Dear all, we are trying to simulate molecule in specified depth in octanol to calculate logP. for this purpose we have used box with slab of octanol, molecule in specified distance in z-axis and this mdp: integrator = md dt = 0.002 tinit = 0 nsteps = 5125000

Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

Thanks Justin, this explains everything. I've got #include "my.ff/forcefield.itp" line in my top file. > My guess is that this is a matter of how the force field was #included in > the > .top file. For instance: > > #include "my.ff/forcefield.itp" > > will match $GMXLIB first, but > > #include "

[gmx-users] lipid-drug simulation question

Hi all, I am simulating drugs in water/lipid bilayer environment. And I have noticed that when I put drug into the middle of the box, it is moving rather quickly around until it finds a x or y boundary. Then it stays there moving not much on both sides of the box. In the first time it looked fine t

[gmx-users] g_rdf

Hi there, I have a problem with g_rdf from version 3.3 I want to be sure, that I have crystal structure or liquid, so I used g_rdf -f full.trr -s full.tpr and selected System System or CA CA But instead of normal radial distribution function, I got only 1 sharp peak at the zero distance and zer