Re: [gmx-users] (no subject)

Hi Justin, I completely dazed over the "download .tgz" option at the top right of the screen. I got all of the files I need for my membrane. Thank you! *Sanim Rahman* On Sat, Mar 18, 2017 at 8:03 AM, Justin Lemkul wrote: > > > On 3/18/17 1:25 AM, Sanim Rahman wrote: > >>

Re: [gmx-users] Pressure problem in EM simulation

Hi, You haven't done a simulation, you've moved down a potential energy surface from one point to another. Of course the potential energy deviates. How much depends how far away from something reasonable you were when you started :-) Mark On Sun, Mar 19, 2017 at 2:19 AM Mishelle Oña

Re: [gmx-users] Pressure problem in EM simulation

On 3/18/17 9:18 PM, Mishelle Oña wrote: Thanks for your answer Justin. Another question for the same simulation. I got this values of potential energy: Average> -127776 Err.Est.>4900 RMSD>12891.3 Tot-Drift> -32877.9 I think the RMSD is way too high. What do you think? Consider the

Re: [gmx-users] Pressure problem in EM simulation

Thanks for your answer Justin. Another question for the same simulation. I got this values of potential energy: Average> -127776 Err.Est.>4900 RMSD>12891.3 Tot-Drift> -32877.9 I think the RMSD is way too high. What do you think? From:

Re: [gmx-users] Pressure problem in EM simulation

On 3/18/17 9:00 PM, Mishelle Oña wrote: Hello! I have a question about pressure in EM simulation. I am using Steepest descent method in a water polymer system. My pressure gets this value: Energy Average Err.Est. RMSD Tot-Drift

[gmx-users] Pressure problem in EM simulation

Hello! I have a question about pressure in EM simulation. I am using Steepest descent method in a water polymer system. My pressure gets this value: Energy Average Err.Est. RMSD Tot-Drift

[gmx-users] Surface tension/pressure calculation

Dear all, I would like to calculate surface tension/pressure of my monolayer simulation. I have two monolayers of lipid each side of a water box. So four interfaces; vaccum/lipid, lipid/water, water/lipid and lipid/vaccum. I used NVT simulation. Is there a way to calculate surface

Re: [gmx-users] Doubt from force constant calculations

On 3/18/17 7:36 AM, Rakesh Pant wrote: Dear Justin, Could you briefly tell how the vibrational analysis is done. Which method and software is generally used. The primary literature for the chosen force field should have this information. -Justin Thanks Rakesh On Fri, Mar 17, 2017 at

Re: [gmx-users] MDRUN doesn't print Hessian Matrix as ordered

On 3/18/17 6:46 AM, Juan José Galano Frutos wrote: On 3/17/17 10:35 AM, Juan José Galano Frutos wrote: * Thank you Justin for your replay. I've read that to compute specific *>* heats (Cv or Cp) it is necessary calculating quantum correction (using *>* the tool g_nmeig). *>* Then, this tool

Re: [gmx-users] (no subject)

On 3/18/17 1:25 AM, Sanim Rahman wrote: Sorry I found this thread here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-September/108197.html From my understanding, I use pdb2gmx on my entire output file, however, where does the data in the .psf file go? You shouldn't

Re: [gmx-users] protein-ligand complex mdrun errors

On 3/17/17 12:43 PM, Vignesh Waran wrote: respected sir, i am using protein-ligand complex tutorials .this my problem .i have all process has been done but like energy minimization result is not coming what we do sir ? my command line gmx mdrun -v -deffnm em how to find the clarify the

Re: [gmx-users] Doubt from force constant calculations

Dear Justin, Could you briefly tell how the vibrational analysis is done. Which method and software is generally used. Thanks Rakesh On Fri, Mar 17, 2017 at 7:16 PM, Justin Lemkul wrote: > > > On 3/17/17 7:53 AM, Rakesh Pant wrote: > >> Dear all, >> >> How to calculate force

[gmx-users] MDRUN doesn't print Hessian Matrix as ordered

On 3/17/17 10:35 AM, Juan José Galano Frutos wrote: >* Thank you Justin for your replay. I've read that to compute specific *>* heats (Cv or Cp) it is necessary calculating quantum correction (using *>* the tool g_nmeig). *>* Then, this tool calculates such a correction using the Hessian matrix.

[gmx-users] Dihedral restraint in explicit water

Dear all, Restraining dihedral for dipeptide in explicit water model, how it can be done? Thank you, Anurag Kumar -- 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

[gmx-users] protein-ligand complex mdrun errors

espected sir, i am using protein-ligand complex tutorials .this my problem .i have all process has been done but like energy minimization result is not coming what we do sir ? my command line gmx mdrun -v -deffnm em how to find the clarify the problem? pls tell me sir GROMACS: gmx

[gmx-users] protein-ligand complex mdrun errors

espected sir, i am using protein-ligand complex tutorials .this my problem .i have all process has been done but like energy minimization result is not coming what we do sir ? my command line gmx mdrun -v -deffnm em how to find the clarify the problem? pls tell me sir GROMACS: gmx