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

, 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

mohammad agha wrote: Thank you very much for your reply. I experienced genbox for gromos force field for my molecules and for dspc molecules in martini tutorial in lipid_tutorial.tar.gz, I took the same warning for all them!!! May I know that what should I do, Please ? Probably nothing

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

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

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

[gmx-users] antifreeze particle in martini coarse-grained

Dear Prof. I have a doubt about my way to add antifreeze water to my system, also I think my question looks silly but please help me for more certainty. I changed W to WF in water.gro file of water that I downloaded from MARTINI site and named that antifreezewater.gro , and with below command

Re: [gmx-users] antifreeze particle in martini coarse-grained

and the other 1000 WF. Your way may work but the original placement of the WF might be silly.  Do not separate the two groups in the mdp file for the temperature control. Leave them together.   On Dec 13, 2011, at 4:09 PM, mohammad agha wrote: Dear Prof. Thanks for your reply. Yes, for example

[gmx-users] coordinate number aroud the first shell

Dear Prof. I want to obtain the coordinate number from the first shell around my cluster, I want to use from integration of the 4*pi*(number density)*area(g(r)r2dr) until the first minimum of the RDF, but I have some questions: Please help me 1- How do I obtain the number density for special

Re: [gmx-users] coordinate number aroud the first shell

- When the only tool you own is a hammer, every problem begins to resemble a nail.   From:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Sunday, 11 December 2011 11:15 PM To: gmx-users@gromacs.org Subject: [gmx-users] coordinate number aroud

[gmx-users] editconf -d

Dear Prof. May I know the best quantity for -d option in editconf program? for example for a cubic box consists of 7 water molecules and 500 surfactant molecules with 22 , 022 , 22 box dimensions in x , y and z? Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Fw: editconf -d

- Forwarded Message - From: mohammad agha mra...@yahoo.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Thursday, December 1, 2011 10:48 PM Subject: editconf -d Dear Prof. May I know the best quantity for -d option in editconf program? for example for a cubic box consists

[gmx-users] g_select

Dear Prof. I have a system consists of 10 micelle after production simulation. How can I select a micelle with 92 monomer? I know that I should use from g_select, but I don't know which argument is proper for me. I also checked -select help in g_select program. Please help me. Best Regards --

Re: [gmx-users] g_select

Thanks for your reply. Best Regards From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 30, 2011 11:27 PM Subject: Re: [gmx-users] g_select mohammad agha wrote: Thanks for your reply

Re: [gmx-users] g_rdf -com

Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, November 27, 2011 3:08 PM Subject: Re: [gmx-users] g_rdf -com On 2011-11-27 12:27, mohammad agha wrote: Dear Prof. I have a question about g_rdf. I have a box consists of 500 surfactants

[gmx-users] g_rdf -com

Dear Prof. I have a question about g_rdf. I have a box consists of 500 surfactants that make 10 micelle. I want to compute rdf for surfactant relative to the center of mass of micelle. When I do g_rdf, the program ask me 2 groups that the first one is COM, but it is COM of molecules that I

[gmx-users] g_clustsize

Dear Prof. I have some problems about g_clustsize program and I didn't find my answer in mailing list. Please help me. I don't know what is the base of selection for -cut option? In my system after doing g_clustsize, when I see nclust.xvg file, it looks like all the atoms in the system were

Re: [gmx-users] g_clustsize

-users] g_clustsize On 2011-11-26 18:55, mohammad agha wrote: Dear Prof. I have some problems about g_clustsize program and I didn't find my answer in mailing list. Please help me. I don't know what is the base of selection for -cut option? In my system after doing g_clustsize, when I see

[gmx-users] editconf -d

Dear Prof. I have a system consists of 500 surfactants + 61000 water beads + 500 ion in martini force field into cubic box with 20.3*20.3*20.3 dimensions, May I know the best quantity for -d option in editconf program to prevent from artificial forces, please? Best Regards Sara -- gmx-users

Re: [gmx-users] density

the micelle COM, and I think that I should use from : N= 4 π ρ∫ 0 00  r2 g(r) dr. , but I don't know how to find N and what is the computation carefully? Please help me.   Best Regards Sara From:Dallas Warren dallas.war...@monash.edu To: mohammad agha mra

[gmx-users] density

Dear Prof. I have problems about density. I equilibrated my system consist 500 surfactants and 6 water molecules in martini coarse-grained for 120 ns and my results of g_energy next pr.mdp for density are: average = 907.701 err.est = 0.61 rmsd = 2.54989 tot-drift = -3.4173 I don't know

[gmx-users] antifreeze water in martini coarse-grained

Dear all, I doubt about gro file of antifreeze water (in martini coarse-grained) that I use for adding to my system. May I ask you send for me a correct gro file of antifreeze water, Please? Best Regards,  SARA-- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] (no subject)

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[gmx-users] question about martini coarse-grained

Dear Gromacs Users, I want to simulate 150 surfactant molecules in the water by MARTINI Coarse-Grained force field, and I have several questions please: 1- I defined 2 groups in index.ndx file named surfactants and w_ion_ wf that second group is consist of water, antifreeze

[gmx-users] question about martini coarse-grained

Dear Gromacs Users, I want to simulate 150 surfactant molecules in the water by MARTINI Coarse-Grained force field, and I have several questions please: 1- I defined 2 groups in index.ndx file named surfactants and w_ion_ wf that second group is consist of water, antifreeze

[gmx-users] question about position restraint in martini coarse-grained

Dear Gromacs Users, I want to simulate 150 surfactant molecules in the water by MARTINI Coarse-Grained force field, and I have several questions please: 1- I defined 2 groups in index.ndx file named surfactants and w_ion_ wf that second group is consist of water, antifreeze

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