[gmx-users] Drude force field

Dear users, How or where can I get the Drude polarizable force field file for current Gromacs version? -- 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] Keep having to path gromacs when opening a new terminal

If you have .bashrc file then just add this line in your .bashrc file then type source .bashrc vi .bashrc *source /usr/local/gromacs/bin/GMXRC* *source .bashrc* ** *Krishna Prasad Ghanta* *Research Scholar* *Molecular Modeling Laboratory*

Re: [gmx-users] Specific heat calculations using gmx energy

Thanks, Prof. Spoel. The Enthalpy does make a sudden drop and excluding that part, the heat capacity values does not differ much with time. However the values still are far from experimental values ( 7934.66 J/mol K* compared to ~ 100 *J/mol K). I am using 5.1.1 version, so I cant use the gmx dos

Re: [gmx-users] Keep having to path gromacs when opening a new terminal

cd /etc/profile.d sudo ln -s /usr/local/gromacs/bin/GMXRC GMXRC.sh On 7/16/2019 8:14 PM, Israel Estrada wrote: Hello Users, I've compiled GROMACS successfully on my machine, but the gmx_mpi command is not recognized until I enter the command source /usr/local/gromacs/bin/GMXRC everything

[gmx-users] Keep having to path gromacs when opening a new terminal

Hello Users, I've compiled GROMACS successfully on my machine, but the gmx_mpi command is not recognized until I enter the command source /usr/local/gromacs/bin/GMXRC everything works fine after, but is there a way I can avoid having to enter that command every time I begin a new session?

Re: [gmx-users] About g_sdf in version 4.6.5.

That is correct. (whoever is Darren? ;) ) Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own

Re: [gmx-users] Specific heat calculations using gmx energy

Den 2019-07-15 kl. 09:24, skrev Pragati Sharma: Dear all, I am simulating a melt of polybutadiene consisting of 60 chains using OPLS forcefield. After 50 ns of NPT production run, specific heat is calculated using the command: *gmx energy -f ener.edr -fluct_props -nmol 60 -driftcorr * and the

Re: [gmx-users] heat capacity collection

Den 2019-07-16 kl. 13:30, skrev Amin Rouy: Hi everyone, I try to collect the heat capacities from my set of simulations. I see that the heat capacity through gmx energy -fluct_props does not provide an output file with the heat capacities. Any suggestion how can I collect them (or how to do

Re: [gmx-users] Flat-bottomed Restrain

Ehsan, That is just a single cylinder, or if you wish you can call it 5 identical overlapping cylinders corresponding to each atom, but that still is just one cylinder. Actually you still have your original *.GRO of your system fed to grompp by -c flag, the reference.gro edited that way is just a

Re: [gmx-users] Flat-bottomed Restrain

Hi, He's set the reference positions (in the -r file), rather than changing the initial positions (with the -c file). Mark On Tue., 16 Jul. 2019, 19:03 ehsan shahini, wrote: > Dear Salman, > > Thanks for the reply. For the first part, you are defining 5 cylinders with > a radius of 1.5. And,

Re: [gmx-users] Xeon Gold + RTX 5000

That is excellent information, thank you. None of us have dealt with AMD CPUs in a while, so would the combination of a Ryzen 3900X and two Quadro 2080 Ti be a good choice? Again, thanks! Alex On 7/16/2019 8:41 AM, Szilárd Páll wrote: Hi Alex, On Mon, Jul 15, 2019 at 8:53 PM Alex wrote:

Re: [gmx-users] Flat-bottomed Restrain

Dear Salman, Thanks for the reply. For the first part, you are defining 5 cylinders with a radius of 1.5. And, I'm not sure about your suggestion for editing the .gro file in that particular manner since there is another option (function 3,4,5) for restraining atoms in a layer. But you are

Re: [gmx-users] Flat-bottomed Restrain

Hi Ehsan, Here is how I understood and would implement the flat-bottom potential; Just suppose you intend to confine a molecule with five atoms in a cylinder with radius of *\rho = 1.500* nm and axes positioned at *x = 3.000 and y = 3.000 nm* parallel to the Z. First you need a posre.rho.itp in

Re: [gmx-users] Flat-bottomed Restrain

Thank you so much for your response. For my first question, are you suggesting using a command like this: gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -r small_molecule.gro -o md.tpr This command, however, results in a warning and a fatal error: WARNING 1 [file

Re: [gmx-users] Xeon Gold + RTX 5000

Hi Alex, On Mon, Jul 15, 2019 at 8:53 PM Alex wrote: > > Hi all and especially Szilard! > > My glorious management asked me to post this here. One of our group > members, an ex-NAMD guy, wants to use Gromacs for biophysics and the > following basics have been spec'ed for him: > > CPU: Xeon Gold

[gmx-users] Hydrogen bond analysis

Hi allI want to carry on a hydrogen bond analysis between a protein and ligand. I tested hbond but it only gives the number of hydrogen bonds which I am not looking for. I want to know exactly which residues are involved in hydrogen bonding and more specifically which atoms of the residues and

[gmx-users] heat capacity collection

Hi everyone, I try to collect the heat capacities from my set of simulations. I see that the heat capacity through gmx energy -fluct_props does not provide an output file with the heat capacities. Any suggestion how can I collect them (or how to do with an script)? thanks -- Gromacs Users

[gmx-users] Generating Ramachandran Plot monitoring movie.

Good Evening Friends, I had some problem with my MD analysis. I want to monitor the Ramachandran plot of some residues. My problem let say I had a tri peptide from which we can get 4 dihedral angles and we can only plot the ramachandran plot for the Mid residue that is second

Re: [gmx-users] force constant (K_fb)

Hi, I would generally not bother. You're already modelling something unphysical. What is the consequence for your observations of either an unexpectedly large range of position, or an uncharacteristic distribution of KE? Mark On Mon., 15 Jul. 2019, 20:13 Alex, wrote: > Dear Gromacs user, >

Re: [gmx-users] Flat-bottomed Restrain

Hi, On Tue., 16 Jul. 2019, 10:32 ehsan shahini, wrote: > Dear all, > > 1. I need to restrain a small molecule in a region (cylindrical) and I want > to restrain all of its atoms in that region. The best tool is flat-bottomed > restrain but it only restrains individual atoms in their

[gmx-users] Flat-bottomed Restrain

Dear all, 1. I need to restrain a small molecule in a region (cylindrical) and I want to restrain all of its atoms in that region. The best tool is flat-bottomed restrain but it only restrains individual atoms in their corresponding regions and not all the atoms in a single region. Hence, if I

Re: [gmx-users] About g_sdf in version 4.6.5.

Darren, so generating SDF over several molecules is possible with the version you mentioned? Sincerely, Henry From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Dallas Warren Sent: Tuesday, July 16, 2019 12:30:19 AM To: GROMACS users