Re: [gmx-users] Center to center distance in cylindrical micelles

You didn't give us much info about your system, so I will assume that your box is a rectangular prism and that all the cylinders are necessarily oriented along the z axis (e.g., because they are "infinite"/periodic). Since the center of mass (COM) of each cylinder must be a point on its axis,

Re: [gmx-users] gmx clustsize

On 8/20/18 3:25 PM, Pandya, Akash wrote: Hi all, I am trying to find out how many clusters I have of my ligand during the course of my trajectory using gmx clustsize. I type the following command and get an error message: gmx clustsize -s glycine.tpr -f glycine.gro -nc nclust.xvg -hc

[gmx-users] gmx clustsize

Hi all, I am trying to find out how many clusters I have of my ligand during the course of my trajectory using gmx clustsize. I type the following command and get an error message: gmx clustsize -s glycine.tpr -f glycine.gro -nc nclust.xvg -hc histo-clust.xvg -mol Program: gmx

Re: [gmx-users] [Install error] What can I do this situation?

On Mon, Aug 20, 2018 at 2:54 PM 김나연 wrote: > There is error messages. TT > 1) What can I do?? > Install manually. The installation warnings suggest that you are risking strange failures (due to mixing C++ libraries). > 2) If this process succeeds, can I do GPU calculations in mdrun? > Yes,

[gmx-users] [Install error] What can I do this situation?

There is error messages. TT 1) What can I do?? 2) If this process succeeds, can I do GPU calculations in mdrun? 3) I think gromacs only supports gcc. But I heard that installing gcc and home-brew at the same time will result in an unknown error. Is that right? Error Messages (In fact,

Re: [gmx-users] Getting ligand's topology

On 8/20/18 2:40 AM, Mahdi Sobati Nezhad wrote: thanks for your taking time. and so on for a begginer like me there is no any way Well, there is if you're willing to invest the time in learning some challenging concepts and some new software. But no one should expect that for any given

Re: [gmx-users] Combining position restraints with Parrinello-Rahman pressure coupling leads to instabilities

On 8/20/18 6:52 AM, Naba wrote: Dear Gromacs users and developers, I am using Gromacs 2018.2. Following the membrane protein simulation tutorial, I am planning to run long simulations of a tetramer that needs larger lipid bilayer than 128 lipids as described in the tutorial. So, I have

[gmx-users] Combining position restraints with Parrinello-Rahman pressure coupling leads to instabilities

Dear Gromacs users and developers, I am using Gromacs 2018.2. Following the membrane protein simulation tutorial, I am planning to run long simulations of a tetramer that needs larger lipid bilayer than 128 lipids as described in the tutorial. So, I have replicated the pre-equilibrated POPC

Re: [gmx-users] force/time application for pull

So, Dear Justin and Mark Basically in Gromacs pulling using umbrella sampling. Force corresponding to the distance increment during constant velocity pulling becomes like. F= k(vt-x) k=spring constant v= constant velocity t=time x= distance between pulled group and reference group. The force

[gmx-users] lipid relaxation time

Dear All, I have a question regarding relaxation time for lipids in simulation. I will be thankful if anyone can help me with this. Actually I want to find the relaxation time so that I can estimate the required time for equilibration before starting production MD. Does anyone know which

Re: [gmx-users] Getting ligand's topology

thanks for your taking time. and so on for a begginer like me there is no any way On Mon, 20 Aug 2018 00:29 Justin Lemkul, wrote: > > > On 8/19/18 10:20 AM, RAHUL SURESH wrote: > > Hi. > > > > First, I feel grimaces users may not entertain other discussions in > grimace > > forum. You can