Re: [gmx-users] Computational electrophysiology issues with membrane leakage

Hi, the output file gives you the numbers of the atoms that seem to move from compartment A to B without passing a channel. I would look at their trajectories and inspect which path they actually take. The channel trimer also needs to be whole at the beginning of the simulation, otherwise the

Re: [gmx-users] Regarding analysing cos theta distribution functions

For making .ndx files look at the following: http://manual.gromacs.org/programs/gmx-make_ndx.html Best of luck, Jonathan On Tue, Apr 11, 2017 at 10:26 PM, Dilip H N wrote: > gmx sorient -f .xtc/trr -s .tpr -n .ndx... > > How to make these indexes for this case..??

Re: [gmx-users] Regarding analysing cos theta distribution functions

gmx sorient -f .xtc/trr -s .tpr -n .ndx... How to make these indexes for this case..?? what are the atoms/groups that i need to consider for indexing in this case.. Sent with Mailtrack

[gmx-users] Regarding analysing cos theta distribution functions

Hello, 1] I want to calculate cos theta distributions (eg.,cos theta distributions of hydrogen's of water in first hydration shell layer of amino acid)..?? 2] and how can i analyze the graph ..?? -- With Best Regards, DILIP.H.N Ph.D Student Sent with Mailtrack

[gmx-users] Computational electrophysiology issues with membrane leakage

Dear all, I’m trying to set up the computational electrophysiology protocol. To do this, I’m trying to replicate the following article http://www.sciencedirect.com/science/article/pii/S0006349511007065 but instead of using g_membed I used a CG approximation (using MARTINI ff + insane script to set

Re: [gmx-users] Density calculation

You have not really defined what you want to obtain all that well. E.g. a mass density is mass per volume, but you seem to take issue with the volume definition. Do you just want to know the mass density in a region that is near the center of your cellulose? If so, you could use gmx traj to get

[gmx-users] Computational electrophysiology issues with leakage

Dear all, I’m trying to set up the computational electrophysiology protocol. To do this, I’m trying to replicate the following article http://www.sciencedirect.com/science/article/pii/S0006349511007065 but instead of using g_membed I used a CG approximation (using MARTINI ff + insane script to set

[gmx-users] Density calculation

Dear all I want to calculate the density of cellulose fibril. My simulation system is cellulose in a box of water and ions. If i apply "gmx energy" after NPT simulation then i will get density of total system which is lower than what expected because of water. "gmx energy -f *.edr -s *.tpr -o

[gmx-users] mdrun (5.1.2) restart doesn't recognize pull-code files given default but unspecified names

Dear users: I noticed some unexpected behaviour with gromacs 5.1.2 and wanted to check here first if it's known and fixed in later versions, or if people consider this behaviour to actually be desirable, before posting a redmine. It's a minor issue. The behaviour might be desirable, since the

Re: [gmx-users] Trying to use cutoff electrostatics with MARTINI

On Tue, Apr 11, 2017 at 1:03 PM, Mark Abraham wrote: > Hi, > > On Tue, Apr 11, 2017 at 12:09 PM Graham J.A. > wrote: > > > Hi, > > > > I'm preparing to do some benchmarking and wanted to look at the > > performance differences between

Re: [gmx-users] Heavy metals parameterisation

On 4/11/17 11:32 AM, Alex Mathew wrote: Thanks, In general for parameterising the small molecules or heavy metals VMD- FFTK is sufficient? or is there any other tools I need to use other than the Gaussian package (for DFT or MP2). You're dealing with really weird systems. You're going to

Re: [gmx-users] Heavy metals parameterisation

Thanks, In general for parameterising the small molecules or heavy metals VMD- FFTK is sufficient? or is there any other tools I need to use other than the Gaussian package (for DFT or MP2). -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Heavy metals parameterisation

On 4/11/17 8:59 AM, Alex Mathew wrote: I'm looking something like this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2856166/ Here the mercury bind to Cys residue and inhibiting the channel. I suggest following a similar method to develop force field parameters, but consistent with

Re: [gmx-users] Heavy metals parameterisation

I'm looking something like this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2856166/ Here the mercury bind to Cys residue and inhibiting the channel. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] Trying to use cutoff electrostatics with MARTINI

Thanks Mark, That makes sense now then, and explains the very small performance difference I'm seeing between the two cases when run out for a bit longer. James On Tue, 2017-04-11 at 11:03 +, Mark Abraham wrote: > Hi, > > On Tue, Apr 11, 2017 at 12:09 PM Graham J.A.

Re: [gmx-users] Heavy metals parameterisation

On 4/11/17 8:44 AM, Alex Mathew wrote: Dear Justin, More specifically, I'm looking for the transport properties of proteins in presence and absence of heavy metals- how heavy metals affecting the transportation of molecules across the channels. Are the transition metals bound to any

Re: [gmx-users] Heavy metals parameterisation

Dear Justin, More specifically, I'm looking for the transport properties of proteins in presence and absence of heavy metals- how heavy metals affecting the transportation of molecules across the channels. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] how to know solvent molecule number

On 4/10/17 10:14 AM, Chintan Bhagat wrote: Dear Justin, As You advised, I tried grep -c option My solvent file - ethanolamine.gro PRODRG COORDS 12 1DRG OAC 1 -0.083 0.327 0.043 1DRG HAE 2 -0.146 0.373 -0.019 1DRG CAB 3 -0.074 0.188 0.009

Re: [gmx-users] Heavy metals parameterisation

On 4/10/17 8:54 AM, Alex Mathew wrote: Thanks Justin, I am looking for the effect of heavy metals in channel proteins. Could you please provide me some links or paper to where i can start QMMM. That's a bit of a broad statement. If you're looking at something like transport through a

Re: [gmx-users] Error during nvt: Not enough memory. Failed to allocate 3425307227 aligned elements of size 4 for grid->grid. What is happening

On 4/10/17 8:12 AM, Li, J. wrote: This error appeared when I tried to do a NVT simulation. The simulation box is 768.0 768.0 768.0 [nm**3], in which there are 9 atoms. There's got to be a ton of void space in that system. 90,000 atoms should fill a box about 100,000 times

Re: [gmx-users] Trying to use cutoff electrostatics with MARTINI

Hi, On Tue, Apr 11, 2017 at 12:09 PM Graham J.A. wrote: > Hi, > > I'm preparing to do some benchmarking and wanted to look at the > performance differences between reaction-field and cutoffs for the > electrostatic model with the MARTINI forcefield. > You'd expect that

[gmx-users] Lennard-Jones parameters for metal surfaces

Hi all, I want to run some simulations of water/metal interfaces, for which I need Lennard-Jones parameters optimized for the metallic atoms in the solid phase (e.g., opposite to as cations in solution). I know of the difficulty of correctly capturing the metal-water interaction with such a

[gmx-users] Trying to use cutoff electrostatics with MARTINI

Hi, I'm preparing to do some benchmarking and wanted to look at the performance differences between reaction-field and cutoffs for the electrostatic model with the MARTINI forcefield. I've downloaded the recommended MDPs from the MARTINI website, but when I specify cutoff in the MDP I still get

[gmx-users] .mdp file settings for thermodynamic integration

Dear Gromacs users I had a doubt regarding .mdp options for free energy using constrained dynamics. If i wish to change a bond length from l_A to l_B (say for example from 0.5 nm to 5 nm. this bond will be used in the form of constraints type 2. something similar to what is shown in manual of