[gmx-users] (no subject)

Hii Everyone I had performed a 100ns protein-ligand (docked complex) simulation with gromacs 5.1.4. The ligand in my case is hydrogen peroxide. I have removed the PBC effect and centered the protein. I have used the following commands: gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o

[gmx-users] restrained md_coordinate issue

commands, the ligand coordinates changes. Can't understand what's wrong!!! Any suggestion is appreciated. Thank You Regards Zaved * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 162, Issue 7

> Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 163, Issue 116

> Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 163, Issue 116

> Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body

[gmx-users] pH dependent simulation

kindly suggest me how to proceed further? Any suggestion is appreciated. Thank You Zaved * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute

[gmx-users] Coulomb-14 Energy

entical whereas it tends to be >>> in >>> different in case of GdmCl. And inspite of the fact that both urea and >>> GdmCl have negative potential. >>> >>> How do we justify this? >>> >>> Thank You >>> >>> Regar

[gmx-users] SDS initial setup

to insert the sds molecules: gmx insert-molecules -f prot.gro -ci sds.pdb -nmol 200 -o comp.gro Will it be appropriate to run simulation with this initial setup? Or do I need to make sure that entire sds molecules are inside the box. Kindly guide me. Thank You Regards Zaved H. * * * D I S C L

[gmx-users] -inter command

> Message: 3 > Date: Thu, 18 Jan 2018 07:39:39 -0500 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] -inter command > Message-ID: <0281054c-c062-90c3-2243-ef0f5f3ed...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 1/18/18

[gmx-users] -inter command

Dear Gromacs Users I have an query regarding gmx pdb2gmx -inter command. Do we use -inter command only for setting the protonation state of charged amino acids in order to perform simulation at different pH? Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology

[gmx-users] Number of glucose molcules

of the simulation box is 10.98 * 10.98 * 10.98 nm. I appreciate any kind response. Regards Zaved * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute

Re: [gmx-users] Number of glucose molecules

ulation box. Can you kindly shed some light on it? Thank You Regards Zaved > People dear to my heart have diabetes, so... > > If you do not mind my asking, are you a high school student, or are you > actually a graduate student/postdoc? If it is the latter, please do the > humanity

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 173, Issue 34

gt; Dear Alex No I am not. I am a Research Student, pursuing from Dept.of Mol Bio and Biotechnology, Tezpur University, India. Thank You Zaved > Please answer my question. Are you a high school student, or do you > actually hold an academic degree from an accredited institution? > &

[gmx-users] ZnO Parameters

Dear Gromacs Users Can anyone provide me the parameters for Zinc Oxide (ZnO)? Thank You Regards Zaved Hazarika PhD Scholar Dept.of Molecular Biology and Biotechnology Tezpur University India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely

[gmx-users] ZnO Parameters

lid state books(for example kittel) Thank you for your kind suggestion. However I didn't found much info from it. > > Thank you. > > > 6 Tem 2018 Cum 13:09 tarihinde ?unu yazd?: > >> Dear Gromacs Users >> >> Can anyone provide me the parameters for Zinc Oxid

[gmx-users] -inter command

> Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body

[gmx-users] -inter command

> Message: 1 > Date: Tue, 16 Jan 2018 08:30:10 +0100 > From: Jo?o Henriques > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] -inter command > Message-ID: >

[gmx-users] SDS initial setup

t I am thinking why then we center the protein (eg and keep it 1 nm from the edge of the box to its center) during protein setup? Thank You Regards Zaved A visualisation to help see what is going on with the PBC and the > molecules https://twitter.com/dr_dbw/status/909559339366572032 > Catch ya, &

[gmx-users] GPU Command

-DGMX_SIMD=AVX2_256 -DGMX_USE_RDTSCP=OFF -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda Do I need to provide any other option (openMPI) while installing groamcs? Thank You Regards Zaved Hazarika PhD Scholar Dept.of Molecular Biology and Biotechnology Tezpur University Indi * * * D I S C L A I M

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 168, Issue 45

3 1 180.000 33.5 2 8 1 2 4 1 180.000 33.5 2 Thank you Regards Zaved Hazarika PhD Scholar Dept.of Molecular Biology and Biotechnology Tezpur University India > Hi, > > Presumably Gdm has atoms connected by three adjacent bonds that general

[gmx-users] GPU Command

auto-selected for this run. Mapping of GPU ID to the 1 PP rank in this node: 0 NOTE: potentially sub-optimal launch configuration, gmx mdrun started with less PP MPI process per node than GPUs available. Each PP MPI process can use only one GPU, 1 GPU per node will be used. Will do PME sum in

[gmx-users] Regarding Coulomb-14 Energy

H 0.33300 0 H22U H 0.33300 0 [ bonds ] OUCUgb_44 CU N1Ugb_45 CU N2Ugb_45 N1U H11Ugb_2 N1U H12Ugb_2 N2U H21Ugb_2 N2U H22Ugb_2 Thank You Regards Zaved > Simply calculate it with Coulomb's Law and apply the 1-4 e

[gmx-users] Coulomb-14 Energy

in case of protein in presence of water and protein in presence of urea are almost identical whereas it tends to be in different in case of GdmCl. And inspite of the fact that both urea and GdmCl have negative potential. How do we justify this? Thank You Regards Zaved Hazarika PhD Scholar Dept.of

[gmx-users] NVT LINCS Warning

16 17 46.60.1001 0.0998 0.1000 16 17 46.60.1001 0.0998 0.1000 16 17 46.60.1001 0.0998 0.1000 N.B. I am using gromacs 5.1.4 version. Any kind suggestion/s will be appreciated. Thank You Regards Zaved Hazarika Research Scholar Dept

[gmx-users] Regarding freezing of NP

Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should

[gmx-users] Freezing Spherical Nanoparticle

Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should

Re: [gmx-users] ramachandran plot

> Message: 5 > Date: Wed, 9 Jan 2019 17:17:31 +0530 > From: Subhomoi Borkotoky > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] ramachandran plot > Message-ID: > > Content-Type: text/plain; charset="UTF-8" Hii Subhomoi Thank you so much for you

Re: [gmx-users] ramachandran plot

anyone suggest me any available tool to analyze ramachandran plot >> timewise for a trajectory? >> >> Thank You >> >> Regards >> Zaved Hazarika >> Research Scholar >> Dept. Of Molecular Biology and Biotechnology, >> Tezpur University, >&

[gmx-users] ramachandran plot

Dear Users Can anyone suggest me any available tool to analyze ramachandran plot timewise for a trajectory? Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and Biotechnology, Tezpur University, India * * * D I S C L A I M E R * * * This e-mail may contain

[gmx-users] Lipid Simulation Analysis

Hello What kind of analysis can we perform for a lipid bilayer simulation? And which are the tools available in gromacs to analyse bilayer simulation? Thank You Regards Z. Hazarika Research Scholar Tezpur University Tezpur ___ D I S C L A I M E R This e-mail may contain