Re: [gmx-users] ZnO Parameters

https://elib.suub.uni-bremen.de/edocs/00104076-1.pdf Page 111. On Tue, Jul 10, 2018 at 7:38 AM, wrote: > > Message: 3 > > Date: Fri, 6 Jul 2018 14:39:15 +0300 > > From: ali akg?n > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] ZnO Parameters > > Message-ID: > >hkwchrutet...@

Re: [gmx-users] ZnO Parameters

Hi, You can fınd parameters on solid state books(for example kittel) Thank you. 6 Tem 2018 Cum 13:09 tarihinde şunu yazdı: > Dear Gromacs Users > > Can anyone provide me the parameters for Zinc Oxide (ZnO)? > > Thank You > > Regards > Zaved Hazarika > PhD Scholar > Dept.of Molecular Biology a

[gmx-users] Generate unit cell

Hello, I have an polymer pdb file, I want to generate crystal unit structure of the pdb file. How can I generate unit cell structure of molecular systems ? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List befor

Re: [gmx-users] Installation error

r CMake build wasn't configured to be able to do the download > that your asking GROMACS to ask CMake to do. > > Mark > > On Sat, Mar 24, 2018, 12:28 ali akgün wrote: > > > Hello, > > > > I got an error in gromacs-5.0.7 installiation cmake part. > > >

[gmx-users] Installation error

Hello, I got an error in gromacs-5.0.7 installiation cmake part. My error is: Scanning dependencies of target fftwBuild Scanning dependencies of target mdrun_objlib Scanning dependencies of target view_objlib [ 0%] Performing pre-download step for 'fftwBuild' [ 0%] Creating directories for 'f

[gmx-users] installation error

Hello, I got an error in gromacs-5.1.5 installiation cmake part. My error is: *** glibc detected *** cmake: free(): invalid pointer: 0x009f241d *** How to fix this error? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_L

[gmx-users] gmx dipole and gmx potential

Hİ all I am newbie and GROMACS, I did some dipole moment and electric potential calculation for water solutions. I want to understand gmx dipole and gmx potential algorithm.I read GROMACS manual 8.5.4 and 8.5.3 but I can not understand about gmx dipole algorithm, so I need information about gmx d

Re: [gmx-users] Pressure through one direction

I mean can i run npt only one direction? On Tue, Nov 28, 2017 at 10:53 PM, Wes Barnett wrote: > On Tue, Nov 28, 2017 at 12:25 PM, ali akgün > wrote: > > > Hi, > > > > Can i generate mdp file for pressure through one direction system.For > > example: > >

[gmx-users] Pressure through one direction

Hi, Can i generate mdp file for pressure through one direction system.For example: Ref pressure: X direction:1.0 bar Other direction: 0.0 bar Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before po

Re: [gmx-users] Build thin film.

nd Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On 24 November

[gmx-users] Build thin film.

I have a pdb file can i build thin film ? -- 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://maillis

Re: [gmx-users] Pressure Fluactiation

I will run with bigger nsteps (like monte carlo :D) , thank you for reply sir. On Wed, Nov 22, 2017 at 11:17 PM, Mark Abraham wrote: > Yes, by running longer, or on a larger system, just as statistical > mechanics predicts. > > Mark > > On Wed, Nov 22, 2017 at 10:16 PM

Re: [gmx-users] Pressure Fluactiation

gy/Pressure > > Mark > > On Wed, Nov 22, 2017 at 9:59 PM ali akgün wrote: > > > Hİ all, > > > > I ran simulation of pvdf(ligand) in solution. My problem is pressure > > fluctuation, My system's pressure fluctuated around reference pressure > and >

[gmx-users] Pressure Fluactiation

Hİ all, I ran simulation of pvdf(ligand) in solution. My problem is pressure fluctuation, My system's pressure fluctuated around reference pressure and average pressure is not equal to my reference pressure. I did well minimisation and nvt run for system before npt run. What should i do about ave

[gmx-users] Pİezoelectricity analyse

Hi, İ am newbie in Gromacs i processed pvdf(polymer) simulation in Gromacs for analyze piezoelectricity effect of pvdf in the different pressure and temperature.(using gmx dipole) Can i process different methods for analyze piezoelectric effect of pvdf. İ only know analyze dipole moments of system