[gmx-users] interface

2012-02-22 Thread mohammad agha
Dear Mark, Thank you very much from your reply. Best Regards Sara From: Mark Abraham To: Discussion list for GROMACS users Sent: Thursday, February 23, 2012 5:24 AM Subject: Re: [gmx-users] interface On 22/02/2012 10:34 PM, mohammad agha wrote: Dear

Re: [gmx-users] interface

2012-02-22 Thread Mark Abraham
To:* Discussion list for GROMACS users *Sent:* Wednesday, February 22, 2012 12:59 AM *Subject:* Re: [gmx-users] interface On 22/02/2012 3:11 AM, mohammad agha wrote: Dear Gromacs Specialists, I made a box consists of water with box lengths: 6nm * 6nm * 6nm , then I equilibrated it with NPT ens

[gmx-users] interface

2012-02-22 Thread mohammad agha
Can you help me to construct the air/water interface, Please? Best Regards Sara From: Mark Abraham To: Discussion list for GROMACS users Sent: Wednesday, February 22, 2012 12:59 AM Subject: Re: [gmx-users] interface On 22/02/2012 3:11 AM, mohammad agha

[gmx-users] interface

2012-02-22 Thread mohammad agha
construct the air/water interface, Please? Best Regards Sara From: Dallas Warren To: Discussion list for GROMACS users Sent: Wednesday, February 22, 2012 4:26 AM Subject: RE: [gmx-users] interface What does it look like when you visualise the coordinate

RE: [gmx-users] interface

2012-02-21 Thread Dallas Warren
-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Wednesday, 22 February 2012 3:12 AM To: Discussion list for GROMACS users Subject: [gmx-users] interface Dear Gromacs Specialists, I made a box consists of water with box lengths: 6nm * 6nm * 6nm , then I equilib

Re: [gmx-users] interface

2012-02-21 Thread Mark Abraham
On 22/02/2012 3:11 AM, mohammad agha wrote: Dear Gromacs Specialists, I made a box consists of water with box lengths: 6nm * 6nm * 6nm , then I equilibrated it with NPT ensemble, box size increased to 6.66176, then I kept the /x-/ and /y-/dimensions fixed, and double the system size in /z

[gmx-users] interface

2012-02-21 Thread mohammad agha
Dear Gromacs Specialists, I made a box consists of water with box lengths:  6nm  * 6nm  * 6nm , then I equilibrated it with NPT ensemble, box size increased to 6.66176, then I kept the x- and y-dimensions fixed, and double the system size in z as following: editconf -f pr1.gro -o newbox1.gro -bo

[gmx-users] interface between Gromacs & CPMD

2008-01-25 Thread Yunan Yan
Dear All, When I try to simulate a QMMM problem with Gromacs/CPMD, the program will stop at the interface "INTERFACE| WAIT FOR CONTINUE-FILE" for all night long. The gromacs part cannot do its part to touch the QMCONTINUE file very well. Is it normal or problematic? Thanks a lot for your attenti