Re: [gmx-users] Simulations with SWM4-DP water model in non PBC

Den 2018-08-11 kl. 16:33, skrev Chi Yuen Pak: Dear GROMACS users, I would like to ask a question concerning about the simulation of a water droplet, with SWM4-DP polarizable water model in nonperiodic boundary conditions. The GROMACS version I use is 2018.2. I have been only able to successfu

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

Hi, Actually, I want to calculate the lattice parameter (distance between two cylinders) of hexagonal phase. Appreciate, if you could help me. Thank you. On Sat, Aug 11, 2018 at 11:11 PM Mark Abraham wrote: > Hi, > > A center is a point. I don't see how you would define a central point of a

Re: [gmx-users] Binding cavity analysis

Hi, I forwarded your email to the GROMACS users list, please use it for user questions. In this way you have a greater chance of getting answers and others can find the questions and answers online. >I have a 2 microsecond trajectory of protein-ligand system. I want to >calculate 3 things: > >1.

[gmx-users] FW: Binding cavity analysis

From: Wycliffe Omwansu [womwa...@gmail.com] Sent: Saturday, August 11, 2018 7:29 AM To: Ullmann, Thomas Subject: Binding cavity analysis Hi, I have a 2 microsecond trajectory of protein-ligand system. I want to calculate 3 things: 1. Time series of number of wa

Re: [gmx-users] Protein-Ligand in bilayer

Hi, None of those are GROMACS tools, so you will probably do better asking elsewhere. But why not generate the topology after the ligands atoms get sorted? Mark On Sat, Aug 11, 2018, 04:18 RAHUL SURESH wrote: > Hi Dr. Mark. > > The docked complex ( docked using auto dock ) when given as input

Re: [gmx-users] Protein-Ligand in bilayer

Can anyone explain the right procedure to be followed while building protein-ligand-popc bilayer? On Sat, Aug 11, 2018 at 6:48 AM RAHUL SURESH wrote: > Hi Dr. Mark. > > The docked complex ( docked using auto dock ) when given as input in > charmm-gui, it ask for either mol2 file or top and prm f

[gmx-users] Simulations with SWM4-DP water model in non PBC

Dear GROMACS users, I would like to ask a question concerning about the simulation of a water droplet, with SWM4-DP polarizable water model in nonperiodic boundary conditions. The GROMACS version I use is 2018.2. I have been only able to successfully run the simulation with only “Group” as the

[gmx-users] No default Ryckaert-Bell. types

Dear All, I experienced an error as follows: (I used the OPLS-AA force field) ERROR 48600 [file topol_Other_chain_C.itp, line 144934]: No default Ryckaert-Bell. types Anyone can help? Kind regards, -- Dr. Baolin Huang Lecturer, School of Life Sciences, Guangzhou Universi

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

Hi, A center is a point. I don't see how you would define a central point of an infinite cylinder. Mark On Sat, Aug 11, 2018, 14:47 Shan Jayasinghe wrote: > Hi, > > I'm sorry for not providing the detail description of my system. Actually > it is a hexagonal phase. Therefore, four cylindrical

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

Hi, I'm sorry for not providing the detail description of my system. Actually it is a hexagonal phase. Therefore, four cylindrical micelles can be seen in a cell. I want to calculate the center to center distance of two cylindrical micelles. On Sat, Aug 11, 2018 at 8:35 PM Mark Abraham wrote: >

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

Shan, Load the .gro file into VMD , select the atoms/residues of interestsee: https://www.youtube.com/watch?v=QV0_CJHBF6U For a plot , You could try converting the trr file to text readable format with trjconv. From there select the atom numbers from each micelle that represent the ce

Re: [gmx-users] RDF calculations for certain atoms in a polymer

Hi Mark, Thank you for your reply! I tried gmx make_ndx -f topol.tpr -o index.ndx before and then selected based on the atom types which worked very well. The only problem is I need to also compute the RDF for the O of the side chain with the same atom type as the ester O in the polymer. Then wi

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

Hi, There is an axis of each cylinder but the two won't be parallel so there is no unique distance to measure. So I suggest thinking carefully about what you really want. Mark On Sat, Aug 11, 2018, 06:58 Shan Jayasinghe wrote: > Hi, > > I tried to used gmx distance. However, I don't understand

Re: [gmx-users] Related to g_enemat command

Hi, I have no idea, but I would read the docs of gmx enemat, and use gmx energy to check that I have the raw energies I want for it. Mark On Sat, Aug 11, 2018, 10:34 ISHRAT JAHAN wrote: > Thanks Mark > I also want to calculate total protein osmolyte interaction energy, then > what should i wr

Re: [gmx-users] RDF calculations for certain atoms in a polymer

Hi, Making a selection with a tool like gmx select or gmx make_ndx is a good way to select e.g. by atomtype. Mark On Sat, Aug 11, 2018, 12:58 Mahsa wrote: > Hello, > > I would like to calculate the RDF between some ions and oxygen atoms of a > polymer. The polymer has ester functional group wi

Re: [gmx-users] periodic-molecules = yes and movie

Thanks. On Wed, Aug 8, 2018 at 10:16 Justin Lemkul wrote: > > > On 8/7/18 8:51 AM, Alex wrote: > > Thanks. > > > > On Tue, Aug 7, 2018 at 8:30 AM Justin Lemkul wrote: > > > >> > >> On 8/7/18 8:23 AM, Alex wrote: > >>> Dear all, > >>> In the simulation of a system in which there is slab, I did n

[gmx-users] RDF calculations for certain atoms in a polymer

Hello, I would like to calculate the RDF between some ions and oxygen atoms of a polymer. The polymer has ester functional group with two different atom types O and OS according to GAFF. It has also a side chain with ethereal oxygen which has the same atom type as the ester part. How can I specify

Re: [gmx-users] Related to g_enemat command

Thanks Mark I also want to calculate total protein osmolyte interaction energy, then what should i write in group.dat file. As i have written 3 Protein Osmolyte Sol And after calculation it gives total protein protein, osmolyte osmolyte, interaction energy. On Sat, Aug 11, 2018, 12:13 PM Mark Abr

Re: [gmx-users] Large differences in calculated and experimental relative hydration free energy.

Hi, No, I have not tried it for a simpler molecule. I thought initially to do something like ethane to ethanol which would be appropriate I guess. But decide to mail to the forum to know if I was missing something obvious. The protocol is based on my understanding of a few papers from Mobley group