[gmx-users] (no subject)

Hii Everyone I had performed a 100ns protein-ligand (docked complex) simulation with gromacs 5.1.4. The ligand in my case is hydrogen peroxide. I have removed the PBC effect and centered the protein. I have used the following commands: gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o

[gmx-users] positioning molecule at desired location

Dear all, I want to keep a water molecule at a particular position of a protein channel. I need to pull this across the channel and observe the energy diagram by PMF. can anyone tell me how I can keep water molecules at a particular position. thank you. -- Gromacs Users mailing list * Please

Re: [gmx-users] npt simulation error

; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 4 On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkul wrote: > > > On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote: > >> Dear Sir >> >> I am trying to simulate protein_ligand complex

Re: [gmx-users] npt simulation error

On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote: Dear Sir I am trying to simulate protein_ligand complex using epsilon = 4 and it is giving the below error What is epsilon = 4? *2 particles communicated to PME rank 4 are more than 2/3 times the cut-off out of the domain

[gmx-users] npt simulation error

Dear Sir I am trying to simulate protein_ligand complex using epsilon = 4 and it is giving the below error *2 particles communicated to PME rank 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x* I have no idea how to solve this

[gmx-users] Doing restart

#yiv4389709560 blockquote, #yiv4389709560 div.yiv4389709560yahoo_quoted {margin-left:0 !important;border-left:1px #715FFA solid !important;padding-left:1ex !important;background-color:white;} Dear gmx users I stoped my md simulation and now i want to restart it. I use gromacs 2016.3  and issued

Re: [gmx-users] how to make molecular model with both ion channel and lipid bilayer?

Charmm-gui.org could help you. Bests, Hadi On Tue, Aug 15, 2017 at 07:55 PM, "Li, Tong" wrote: Dear all, I am trying to make a model of ion channel with cell membrane. Is there a specific software to make this? I mean just the coordination file. VMD can generate the membrane automatically, I

[gmx-users] how to make molecular model with both ion channel and lipid bilayer?

Dear all, I am trying to make a model of ion channel with cell membrane. Is there a specific software to make this? I mean just the coordination file. VMD can generate the membrane automatically, I can find the 'pdb' files of ion channels, but I have no idea how to combine them. Thanks all,

[gmx-users] (Don't know if mail worked last time)Drift with groups+tabulated potential.

Dear GROMACS Community, First of all, if someone got this email twice, I am sorry. It is my first post and I was not sure if it worked. I am trying to do a simulation using a tabulated potential which forces me to use the group cut-off. I get a drift in the conserved quantity of

Re: [gmx-users] Fwd:

On 8/15/17 1:52 AM, saranya wrote: Hi, I have done protein-drug simulations for 100ns. While calculating the hydrogen bond between the protein-drug complex I am getting only 2 hydrogen bonds. The number of H-bond formation is very low I have a question about is there any influence of the drug