Re: [gmx-users] calculation of density for martini coarse-grained

2011-12-16 Thread Tsjerk Wassenaar
gmx-users@gromacs.org Sent: Thursday, December 15, 2011 10:28 PM Subject: Re: [gmx-users] calculation of density for martini coarse-grained Thank you very much. Best Regards Sara From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS

Re: [gmx-users] calculation of density for martini coarse-grained

2011-12-15 Thread mohammad agha
AM Subject: Re: [gmx-users] calculation of density for martini coarse-grained On 15/12/2011 5:59 PM, mohammad agha wrote: Dear Prof. May I ask you two questions, Please? 1- I work with MARTINI force field. I have a surfactant molecule consists of 5 beads. After I placed 151 surfactants

Re: [gmx-users] calculation of density for martini coarse-grained

2011-12-15 Thread Mark Abraham
, 2011 11:19 AM *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained On 15/12/2011 5:59 PM, mohammad agha wrote: Dear Prof. May I ask you two questions, Please? 1- I work with MARTINI force field. I have a surfactant molecule consists of 5 beads. After I placed 151

Re: [gmx-users] calculation of density for martini coarse-grained

2011-12-15 Thread mohammad agha
, December 15, 2011 6:31 PM Subject: Re: [gmx-users] calculation of density for martini coarse-grained On 16/12/2011 1:36 AM, mohammad agha wrote: Dear Prof. Thank you for your reply. I'm really sorry for my mistake in writing the density!! my calculated density become: 90.254026 gr/l while

Re: [gmx-users] calculation of density for martini coarse-grained

2011-12-15 Thread Justin A. Lemkul
@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Thursday, December 15, 2011 11:19 AM *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained On 15/12/2011 5:59 PM, mohammad agha wrote: Dear Prof. May I ask you two questions, Please? 1- I work with MARTINI force field. I have

Re: [gmx-users] calculation of density for martini coarse-grained

2011-12-15 Thread Justin A. Lemkul
jalem...@vt.edu *To:* mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, December 15, 2011 9:26 PM *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained mohammad agha wrote: Dear Prof. Thank you very much

Re: [gmx-users] calculation of density for martini coarse-grained

2011-12-15 Thread mohammad agha
Thank you very much. Best Regards Sara From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 15, 2011 10:02 PM Subject: Re: [gmx-users] calculation of density for martini coarse-grained

Re: [gmx-users] calculation of density for martini coarse-grained

2011-12-15 Thread mohammad agha
From: mohammad agha mra...@yahoo.com To: jalem...@vt.edu jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 15, 2011 10:28 PM Subject: Re: [gmx-users] calculation of density for martini coarse-grained Thank you very

[gmx-users] calculation of density for martini coarse-grained

2011-12-14 Thread mohammad agha
Dear Prof. May I ask you two questions, Please? 1- I work with MARTINI force field. I have a surfactant molecule consists of 5 beads. After I placed 151 surfactants into my simulation box (cubic) with length of 10 nm, Gromacs reported: Volume = 1000 nm3 Density = 15.8111 gr/l My volume is

Re: [gmx-users] calculation of density for martini coarse-grained

2011-12-14 Thread Mark Abraham
On 15/12/2011 5:59 PM, mohammad agha wrote: Dear Prof. May I ask you two questions, Please? 1- I work with MARTINI force field. I have a surfactant molecule consists of 5 beads. After I placed 151 surfactants into my simulation box (cubic) with length of 10 nm, Gromacs reported: Volume =