Re: Re: [gmx-users] User specified potential functions

Hi Mark I transfered all the table files with the dos2unix tool, and it worked. Thank you so much! Best regards! 2012-08-27 toby1024 Message: 2 Date: Mon, 27 Aug 2012 08:31:55 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] User specified potential functions

[gmx-users] User specified potential functions

4.0959976654E+15 9.8303939301E+17 Any suggestions are welcome! Thank you in advance! 2012-08-25 toby1024 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http

[gmx-users] freeze the carbonyl carbon atoms

and oxygen atoms are supposed to have bond interactions. I can freeze the rest carbon atoms of the CNT, but how to deal with the carbonly atoms? Any suggestions are appreciated! Thank you in advance! 2011-05-09 toby1024 -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Re: gmx-users Digest, Vol 85, Issue 67

for this idea? Thank you! 2011-05-09 toby1024 Message: 4 Date: Mon, 09 May 2011 06:58:04 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] freeze the carbonyl carbon atoms To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4dc7c8bc.5090...@vt.edu

[gmx-users] Re: freeze the carbonyl carbon atoms

I intend to apply an electric filed on the whole system and the possitive oxygen will be certainly affected. 2011-05-09 toby1024 Message: 5 Date: Mon, 09 May 2011 22:38:48 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] freeze the carbonyl carbon atoms

[gmx-users] using command g_traj to output the trajectory of an ion in the z direction

Hi I am trying to use g_traj to output the trajectory of an ion in the z direction. I used the following command: g_traj_mpi -f cntsol2.trr -s cntsol2.tpr -n cntsol.ndx -z -ox K_nojump.xvg For the option '-z', the manual describes it as 'Plot Z-component'. However, I still got the trajectory

[gmx-users] SMD simulations stops without error

Hi I pulled an ion to move along the axial direction in a nanotube by using SMD simulation, with the version of Gromacs-4.0.7. For some cases, the simulations stopped without any errors. The simulation could properly run, but it did not run to the end. The following is the pulling code in my

[gmx-users] Steered Molecular Dynamics (SMD)

Dear all: These days, I am trying to pull a slab of griphene moving along the Z direction at a constant speed. The slab of griphene contains 700 atoms. After several times of E-mail communication with the Gromacs users, the simulation can run. However, the run didn't produce the results which

[gmx-users] Re: Steered Molecular Dynamics (SMD) in Gromcas-4.0.5(toby10222...@sina.com)

Dear all: These days, I am trying to pull a slab of griphene moving along the Z direction at a constant speed. The slab of griphene contains 700 atoms. After several times of nbsp;E-mail communication with the Gromacs users, the simulation can run. However, the run didn't produce the results

[gmx-users] Re: Steered Molecular Dynamics (SMD) in Gromcas-4.0.5(toby10222...@sina.com)

Hi Carsten: Thank you for your answers. I don't know whether I am right to reply to gmx-us...@gromacs.org. If I am wrong, please tell me. As in my last letter, I said I was not able to set pull_weights1 correctly. I have red the mannual, but I don't understand what it tells. I'll do with your

[gmx-users] Steered Molecular Dynamics (SMD) in Gromcas-4.0.5

nbsp; Dear all: nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; I’m using Gromacs-4.0.5 and I want to use the pull code to pull a slab of griphene to move along the Z direction in the simulation (Steered Molecular Dynamics-SMD). The griphene has 700 carbon atoms and the positions of the 700 atoms are expected

[gmx-users] Insert a certain number of water molecules into a nanotube

nbsp;Dear all: nbsp; nbsp;nbsp;nbsp;nbsp; I am trying to insert a certain number of water molecules into a nanotube with Gromacs-4.0.5. When I input the command genbox -cp tube.gro -ci spc216.gro -nmol 328 -try 20 -o, I get the following error. nbsp; Program genbox, VERSION 4.0.5 Source code

[gmx-users] How to freeze the atoms?

nbsp;Dear all nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; I attach 8 carbonyl groups onto a carbon nanotube (CNT). Each carbonyl group is considered as a residue named Car and each carbon atomnbsp;in the CNT is considered as a residue named Gr1. In the mdp file, the freezegrps are Gr1 and Car, and the