Re: [gmx-users] simulation at different temperature

Dear Justin, Thanks for the reply, Could you tell me what is the unique purpose of the REMD and where I can learn it from basics? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 24

... well, this URL under ans.2 (http://www.bevanlab.biochem. vt.edu/Pages/Personal/justin/gm) isn't working. 404 Not Found is what I'm repeatedly getting. Please rectify/improve. Thanks and regards! *Amitabh Jayaswal* *PhD Bioinformatics Scholar* *Banaras Hindu University* *Varanasi, U.P., India

Re: [gmx-users] simulation at different temperature

Sure, and I suggested that alternative. Alex On Wed, Jul 5, 2017 at 3:45 PM, Justin Lemkul wrote: > > > On 7/5/17 3:09 PM, Alex wrote: > >> I don't understand the objection. This _is_ full dynamics of the system >> containing behavior at all desired temperatures. >> After it's

Re: [gmx-users] Number of ions in Anionic lipid system- Charmm-GUI

On 7/5/17 12:17 PM, Nidhin Thomas wrote: Hi Justin, Thanks a lot for the prompt reply. I used just 400 POPC lipids to build the lipid bilayer and when I added 150 mM KCl, it added 49 K+ and 49 Cl- to the system. Do you think these numbers are correct? Could you please tell me how I can

Re: [gmx-users] gromacs.org_gmx-users Digest, Acetonitrile with CHARMM ff

On 7/5/17 10:47 AM, Sonia Milena Aguilera Segura wrote: On 7/5/17 5:15 AM, Sonia Milena Aguilera Segura wrote: Dear GROMACS users, I am currently interested in studying properties of some solvents, among them acetonitrile and isopropanol. I would like to use CHARMM force field for

Re: [gmx-users] simulation at different temperature

On 7/5/17 3:09 PM, Alex wrote: I don't understand the objection. This _is_ full dynamics of the system containing behavior at all desired temperatures. After it's done, you can easily split trajectories into the desired annealing regions. Alternatively, you could simply script this as a

Re: [gmx-users] TIP4P/ice pdb file

I believe that you can use any 4-point water model .gro for any 4-point water topology (or likewise for 3-point water models). Did you try it yet? If so, what problem are you running into specifically? From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

[gmx-users] TIP4P/ice pdb file

Dear All, I would like to simulate water using TIP4P/ice potential. My question is that how can I generate .gro file for this simulation? I will use TIP4P/ice topology that is available in SklogWiki, but I cannot understand how can I generate .gro file for this topology. Can I easily use

Re: [gmx-users] simulation at different temperature

Dear Alex, I guess this is annealing and which will give only one output.xtc, I'm looking for full dynamics of the system (say 100 ns for each temperature, 300 K,305 K340 K ). Further, I need to compare the results with each other. Thank you. -- Gromacs Users mailing list * Please search

Re: [gmx-users] simulation at different temperature

Of course: http://manual.gromacs.org/online/mdp_opt.html -- see 'simulated annealing'. Alex On 7/5/2017 11:45 AM, Alex Mathew wrote: Dear gmx users, I would like to see the temperature dependence of an ion channel/membrane protein in lipid bilayer system. My plan is to run a simulation at

[gmx-users] simulation at different temperature

Dear gmx users, I would like to see the temperature dependence of an ion channel/membrane protein in lipid bilayer system. My plan is to run a simulation at 300 K to 340 K by increasing 5 K and observing the permeation of molecules, pore diameter, sec structure .etc. Are there any techniques

[gmx-users] Number of ions in Anionic lipid system- Charmm-GUI

Hi Justin, Thanks a lot for the prompt reply. I used just 400 POPC lipids to build the lipid bilayer and when I added 150 mM KCl, it added 49 K+ and 49 Cl- to the system. Do you think these numbers are correct? Could you please tell me how I can check the correct number of ions? The size of

[gmx-users] Charge Mutation (State B) for Ions

Dear all, I am doing a FEC via alchemical transformation. In order to keep the charge constant I plan to mutate ions at the same time. In particular, I want to change the charge of MG ions. My question is did I manipulate the .top .itp and .gro file in the right way: In the topology.top

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 165

Dear Hannes, Thank you very much for your reply, really appreciated. > Date: Mon, 26 Jun 2017 12:09:45 +0100 > From: Hannes Loeffler > To: > Cc: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Fwd: Relative free energy

Re: [gmx-users] gromacs.org_gmx-users Digest, Acetonitrile with CHARMM ff

> On 7/5/17 5:15 AM, Sonia Milena Aguilera Segura wrote: > > Dear GROMACS users, > > > > I am currently interested in studying properties of some solvents, among > > them acetonitrile and isopropanol. I would like to use CHARMM force field > > for compatibility with other molecules and I am

[gmx-users] EQUILIBRATION

HiI am a new GROMACS user and trying to run md on HDAC2 with PDB ID: 4LY1.  but when I wanted to performance equilibration , i got this ERROR: step 1: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if

[gmx-users] Hydroxyapatites parameter

Dear gmx users, I would like to simulate hydroxyapatites with biological molecules. How can I simulate this type of systems using groamcs? Are there any parameters for hydroxyapatite? Please. Best regards, -- Gromacs Users mailing list * Please search the archive at

[gmx-users] the sum of the two largest charge group radii is larger than rlist

Hi, I get the following error: " Largest charge group radii for Van der Waals: 6.762, 6.758 nm Largest charge group radii for Coulomb: 9.487, 9.465 nm WARNING 1 [file md_vsIonDod.mdp]: The sum of the two largest charge group radii (18.951988) is larger than rlist (1.40) " I found

Re: [gmx-users] Flat-bottom spherical potential

On 7/5/17 8:36 AM, Shraddha Parate wrote: Hello all, I had emailed to Gromacs Users List the following query as per the attached thread (https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx- users/2017-June/114166.html) Justin mentioned about applying a flat-bottom spherical potential

Re: [gmx-users] Acetonitrile and isopropanol with CHARMM ff

On 7/5/17 5:15 AM, Sonia Milena Aguilera Segura wrote: Dear GROMACS users, I am currently interested in studying properties of some solvents, among them acetonitrile and isopropanol. I would like to use CHARMM force field for compatibility with other molecules and I am taking my initial

Re: [gmx-users] methylated HSP

On 7/4/17 1:32 PM, Emma Ahlstrand wrote: Hi, I am going to simulate a protein with a methylated histidine in Gromacs using CHARMM36 FF. I name the modified aminoacid HIC, the structure is attached in pdf file. I have followed the discussion in

Re: [gmx-users] Automake problem during installation 4.5.7

On 7/4/17 11:56 PM, CHEN, Yu Wai [ABCT] wrote: Dear all, I am trying to install 4.5.7 (because I need to use a forcefield which is for 4.5.X) with MPI on our system Any force field that is in the format of version 4.5 is compatible with all newer GROMACS versions. I recommend that you

Re: [gmx-users] Number of ions in Anionic lipid system- Charmm-GUI

On 7/4/17 9:20 PM, Nidhin Thomas wrote: Dear GROMACS Users, I have created a lipid bilayer system (300 POPC + 100 POPG) using CHARMM-GUI. I want to include 0.150 M KCl in the system. When I use the option in charmm-gui, it gives 98K+ ions and -2 Cl ion. But when I calculated the number of

Re: [gmx-users] Ligand and ion topology

On 7/4/17 5:33 AM, Khadija Amine wrote: Dear gromacs users, I have a protein with GNP ligand and acetate ACT ion that I want to simulate. I have prepared topologies for both GNP and ACT with PRODRG program. Don't use PRODRG unless you manually reparametrize the charges and charge groups

Re: [gmx-users] 5' Phosphate (5PHO) patch for RNA in CHARMM36 forcefield - Gromacs

On 7/4/17 12:31 AM, SOMNATH JAN wrote: Dear Users, I am trying to run a MD simulation in Gromacs using CHARMM36 forcefield for a RNA that has phosphate (P, OP1, OP2, OP3) on 5' . As the charmm36 forcefield doesn't recognize the phosphate atom (OP3) on 5' of RNA, pdb2gmx is giving an error. And

Re: [gmx-users] protein protein interaction: side chain contribution

On 7/3/17 4:20 AM, Tushar Ranjan Moharana wrote: Hi all, I want to know the contribution of various amino acid side chain in complex that composed of 2 proteins. I used GROMOS53a6 forcefiel for the simulation. All parameters are as recommended by the concerned paper. I made separate index

[gmx-users] Flat-bottom spherical potential

Hello all, I had emailed to Gromacs Users List the following query as per the attached thread (https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx- users/2017-June/114166.html) Justin mentioned about applying a flat-bottom spherical potential which will keep the droplet formed on the surface.

[gmx-users] Gromacs 5.0 - Solvent Accessible Surface Area (sasa) separate Hydrophobic and Hydrophilic components

Hi, I would like to measure the Hydrophobic and Hydrophilic components of the Solvent Accessible Surface Area. In the Tool Changes for 5.0 I found these command: gmx sasa -s md.tpr -f md_traj.trr -surface 'group "A"' -output '"Hydrophobic" group "A" and charge {-0.2 to 0.2}; "Hydrophilic" group

[gmx-users] Acetonitrile and isopropanol with CHARMM ff

Dear GROMACS users, I am currently interested in studying properties of some solvents, among them acetonitrile and isopropanol. I would like to use CHARMM force field for compatibility with other molecules and I am taking my initial structure files from virtualchemistry.org. Does someone know