[gmx-users] System shrinkage during vacuum simulation

close to the original dimension in the z direction as soon as the simulation started after I analyzed it using g_energy. Is there a mistake with my production .mdp file? I will truly appreciate your assistance. Regards, Sanim Rahman -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] Plotting Density Over Time?

. Regards, Sanim Rahman -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman

Re: [gmx-users] GROMACS and SIMtoEXP

Thank you David, I realized my mistake and I need to be using number density when working with SIMtoEXP however, I was wondering if there is some script out there to easily convert my number density from gromacs to the compatible file format for SIMtoEXP. Regards, Sanim Rahman On Wed, Jun 21

[gmx-users] Using PME with Slab Boundaries

have seen simulations using PBC in all three dimensions with slab boundaries with PME. What are the consequences of running a simulation with slab geometry and pbc in all three dimensions with PME? Regards, Sanim Rahman -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] Technqiues for Applying Assymmetric Ion Concentrations?

as such. The membrane system that I am using is from CHARMM-GUI. I will truly appreciate your input. Regards, Sanim Rahman -- 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 http

Re: [gmx-users] Deuterium Order Parameter Calculations

electrostatic potential on a membrane solvated in KCl. If I want to do this, what index group would I use? Regards, Sanim Rahman On Tue, May 30, 2017 at 8:13 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/30/17 7:16 PM, Sanim Rahman wrote: > >> Hello everyone, >&

[gmx-users] Deuterium Order Parameter Calculations

with the command and I received "NaN" values for two of my carbons for my calculations on Sn1. I will truly appreciate your response and assistance. Regards, Sanim Rahman *Sanim Rahman* B.S. Chemical Engineering, 2019 Resident Assistant, Castor Hall Engineering Living Learning Community 2016-2017

[gmx-users] Deuterium Order Parameter Analysis

"NaN" values for two of my carbons for my calculations on Sn1. I will truly appreciate your response and assistance. Regards, Sanim Rahman -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

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 <jalem...@vt.edu> wrote: > > > On 3/18/17 1:

Re: [gmx-users] (no subject)

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? *Sanim Rahman* B.S. Chemical Engineering, 2019 Resid

[gmx-users] (no subject)

Name* *Protein* *[ molecules ]* *; Compound#mols* *Other 1* *Water 1* I recalled implementing the same technique in one of the GROMACS tutorials, but I am unsure what I am doing differently in my approach to receive this error. Thank you. I will truly apprecia

[gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing

and CHARMM36? I read a previous thread that you can't have two [ default ] lines which make sense but I am unsure of what is the proper protocol to get around this to include both force fields. Any help will be deeply appreciated! Thank You, *Sanim Rahman* B.S. Chemical Engineering, 2019 Resident

Re: [gmx-users] GRO File Merging

Rahman* B.S. Chemical Engineering, 2019 Resident Assistant, Castor Hall Engineering Living Learning Community 2016-2017 Co-Founder and Co-President of the Undergraduate Research Society Undergraduate Researcher, Global Center for Hearing and Speech Research <https://www.linkedin.com/pub/sanim-rah

[gmx-users] GRO File Merging

hen combining topology files, I would convert lipid.top and solvent.top into .itp files and use the #include statement to combine them into my protein.top file? After that, my system should be set correct? Thank You, Sanim Rahman -- Gromacs Users mailing list * Please search the archive at h

Re: [gmx-users] Issues combining protein and membrane file?

14 system_inflated.gro 5 area.dat Here are the files I attached: Original- https://www.dropbox.com/s/aaj4q4efrjxmj3b/system.gro?dl=0 Inflated- https://www.dropbox.com/s/aiu89i1n5nj5bpp/system_inflated.gro?dl=0 Regards, Sanim Rahman On Sat, Feb 18, 2017 at 7:22 PM, Justin Lemkul <ja

Re: [gmx-users] Issues combining protein and membrane file?

Thank you Justin, I was able to remove the velocities from my file but it still fails to read. I attached a dropbox link to my file if you have the time to take a look at it. https://www.dropbox.com/s/aaj4q4efrjxmj3b/system.gro?dl=0 Thank you! Regards, Sanim Rahman On Sat, Feb 18, 2017 at 5

[gmx-users] Issues combining protein and membrane file?

331 3.921 0.4792 -0.0093 -0.0879 I updated the number of atoms in my system and removed nonessential lines as well. Also, would the inflategro procedure be appropriate for this simulation considering that I am inserting a +10,000 atom protein into a lipid membrane? Regards, *Sanim Rah

Re: [gmx-users] Deletion of Lipids During InflateGro?

as 256 lipids. I compared my popc_inflated.gro file to my popc.gro file inflated under the same parameters. They were exactly the same. Thank you for your assistance. Regards, Sanim Rahman On Fri, Dec 30, 2016 at 11:55 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/29/16 10:32 P

[gmx-users] Deletion of Lipids During InflateGro?

separate pieces. Is there a way to have the script avoid reducing the number of lipids in the system in my original method? I will deeply appreciate your assistance! -Sanim Rahman -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

Re: [gmx-users] Removal of Waters in Hydrophobic Core

for the assistance! I deeply appreciate the time you have spent with my situation. Regards, *Sanim Rahman* B.S. Chemical Engineering, 2019 Undergraduate Researcher, Global Center for Hearing and Speech Research <https://www.linkedin.com/pub/sanim-rahman/108/a64/986> On Mon, Nov 28, 2016 at 9

Re: [gmx-users] Removal of Waters in Hydrophobic Core

that the bilayer_separator.pl script could complement the keepbyz.pl script perfectly. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html Let me know if you would like me to send my current script and the image of the current model. Regards, *Sanim Rahman* B.S. Chemical

Re: [gmx-users] Removal of Waters in Hydrophobic Core

the water molecules will be removed. Other than that, do you have any suggestions? *Sanim Rahman* B.S. Chemical Engineering, 2019 Undergraduate Researcher, Global Center for Hearing and Speech Research On Fri, Nov 25, 2016 at 3:48 PM, Christopher Neale < chris.ne...@alum.utoronto.ca> wro

[gmx-users] Removal of Waters in Hydrophobic Core

ez < $lowerz" | bc` myno=$(expr $nolx + $nohx) if [ "$myno" != 0 ]; then z=${#first} if [ "$z" != 8 ]; then sfirst="[[:space:]]$first" else sfirst=$first fi `echo grep $sfirst $1` fi done I will appreciate the help! Regards

[gmx-users] Post Permission

Hello, I would like access to post to the mailing list. Thank you! Regards, *Sanim Rahman* B.S. Chemical Engineering, 2019 Resident Assistant, Castor Hall Engineering Living Learning Community 2016-2017 Undergraduate Researcher, Global Center for Hearing and Speech Research Honors College