[gmx-users] Order parameter for unsaturated lipid chain in UA model

Dear gmx users, I am sorry to ask this question again, but reading in the email achieve did not enlighten me. I found this email which describes my problem, but unfortunately it has no replies: http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html Also there are these two

SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel

Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul Sendt: to 25-02-2010 14:42 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel Sarah Witzke wrote: Dear gmx users, I am sorry to ask

[gmx-users] spc vs. flex_spc

Dear gmx-users, I am wondering whether or not there is a good reason to use flex_spc during energy minimisation and spc during production run? I guess one would not use flex_spc during a production run as this would decrease the time step needed quite a lot - but is it a good idea to use

SV: [gmx-users] spc vs. flex_spc

Thank you very much for your quick answer Berk! Fra: gmx-users-boun...@gromacs.org på vegne af Berk Hess Sendt: ma 15-02-2010 10:56 Til: Discussion list for GROMACS users Emne: RE: [gmx-users] spc vs. flex_spc Hi, flex_spc is not a reliable water model, never

[gmx-users] Closing of .trr and .edr files after running out of space

Dear gmx-users, I have been very unfortunate (and stupid): I was running a simulation of 220 ns and due to limited space at our cluster-computer I was writing the .trr file and .edr file directly to another disc. That was un-clever since I did not write the .cpt file to that disc as well. As I

RE: [gmx-users] Closing of .trr and .edr files after running out ofspace

Thank you very much, that was a good idea! I tried ~/gromacs-4.0.4/bin/trjconv -f dmpc.trr -e 15 -o dmpc-150ns.trr to get the first 150 ns out of the simulation. Trjconv writes this to me: Will write trr: Trajectory in portable xdr format trn version: GMX_trn_file (single precision) -

[gmx-users] Principal axis (g_principal)

Dear gmx users, I am doing several analyses (version 4.0.4) on my simulations with small organic molecules inserting into a DMPC bilayer. Now I would like to calculate whether the small molecule inserts into the membrane with a specific angle to the membrane normal (or z-axis). I have used two

SV: SV: SV: SV: [gmx-users] g_saltbr

Sarah Witzke wrote: snip In each of the files are a set of distances as a function of time - it does not seem that strange, that the size is equal then. When I plot for instance the four .xvg files mentioned above I get four different curves. Also diff lists that every line is different

SV: SV: SV: SV: [gmx-users] g_saltbr

salt bridges between them. Seems to add up, doesn't it? Probably should be considered a bug though. Better file it... Cheers, Tsjerk On Wed, Dec 2, 2009 at 7:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sarah Witzke wrote: snip In each of the files are a set of distances as a function

SV: [gmx-users] g_saltbr

in advance, Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Sarah Witzke Sendt: fr 20-11-2009 14:55 Til: jalem...@vt.edu; Discussion list for GROMACS users Emne: RE: [gmx-users] g_saltbr -Original Message- From: gmx-users-boun...@gromacs.org

SV: SV: [gmx-users] g_saltbr

Sarah Witzke wrote: Dear gmx users, I'm sorry to continue an old thread - here's a summary: I have a DMPC bilayer surrounded by water and a small organic molecule with a deprotonated carboxylic acid. The small molecule diffuses near the membrane interface/into the membrane. I would like

[gmx-users] g_saltbr

Dear gromacs users, First of all thank you for all your previous help! I have a new question regarding an analysis of ionic interactions between DMPC lipids and a small molecule with a deprotonated carboxylic acid. g_saltbr takes as input an .xtc file and a .tpr file and from these files it

RE: [gmx-users] g_saltbr

-Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Fri 20-11-2009 14:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_saltbr Sarah Witzke wrote: Dear gromacs users, First of all thank you for all your previous help! I

RE: SV: SV: SV: [gmx-users] Hydrogen bonding

-Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Thu 19-11-2009 02:09 To: Gromacs Users' List Subject: Re: SV: SV: SV: [gmx-users] Hydrogen bonding Sarah Witzke wrote: Sarah Witzke wrote: snip ARRGH, I'm sorry, things went too

SV: [gmx-users] Hydrogen bonding

Sarah Witzke wrote: Dear gmx-users, I have done simulations of one small molecule that diffuses into a DMPC membrane. This small molecule contains an alcohol group and is therefore capable of hydrogen bonding to the oxygens of DMPC (phosphate and glycerol region). I have read the manual

SV: SV: [gmx-users] Hydrogen bonding

Sarah Witzke wrote: snip Yes, I see this. Do you by the way know why this .ndx files under the title [ donors_hydrogens_DMPC ] lists a lot of non-heteroatoms (carbon atoms)? No clue. Probably the code identifies the functional group to which the donor belongs. The more pertinent

SV: SV: SV: [gmx-users] Hydrogen bonding

Sarah Witzke wrote: snip ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per hbond is 628.571 ps? Yes, per the calculation. For a bit more about the analysis, see the Please read and cite notices, as well as this thread: http://lists.gromacs.org/pipermail/gmx

[gmx-users] Hydrogen bonding

Dear gmx-users, I have done simulations of one small molecule that diffuses into a DMPC membrane. This small molecule contains an alcohol group and is therefore capable of hydrogen bonding to the oxygens of DMPC (phosphate and glycerol region). I have read the manual (section 8.12 and

[gmx-users] g_bundle to calculate angle with z-axis

Dear gromacs users, I am conducting an analysis on my system consisting of a DMPC bilayer with small organic molecules inserting into it. The small molecule consists of a ring with two substituents opposite each other (like para for a benzene ring). Below I have tried to sketch the ring of

SV: [gmx-users] g_bundle to calculate angle with z-axis

| / \ | | \ / | 1 Best, Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Sarah Witzke Sendt: sø 08-11-2009 20:49 Til: Discussion list

RE: [gmx-users] Z-position calculation

Hi, To get the z coordinate of the center of mass of a molecule I use the following command: echo number of molecule | g_traj -f xxx.xtc -s xxx.tpr -n xxx.ndx -nox -noy -com -ox xxx.xvg I guess you can create an .ndx file for a lipid head group to get the z coordinate of this. Regards,

SV: [gmx-users] Error message: Cut-off length is longer than halfthe shortest box vector

Which version of gromacs are you using? If you are using version 4.0 editconf will change your box dimensions to zero. Fra: gmx-users-boun...@gromacs.org på vegne af Mark Abraham Sendt: ti 29-09-2009 05:48 Til: Discussion list for GROMACS users Emne: Re:

SV: [gmx-users] diffusion coefficient with g_msd

:34 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] diffusion coefficient with g_msd On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote: Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate

SV: SV: [gmx-users] diffusion coefficient with g_msd

Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 13:32 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] diffusion coefficient with g_msd Sarah Witzke wrote: Dear XAvier, Thank you very much for your answer. I have posted my .mdp file

[gmx-users] diffusion coefficient with g_msd

Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate the diffusion coefficient of the molecules inside the membrane, and therefore I looked at g_msd. The manual (version 4.0) states on p. 250 (manual

FW: [gmx-users] One more broken .trr file

-Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Sat 21-03-2009 13:20 To: Discussion list for GROMACS users Subject: Re: [gmx-users] One more broken .trr file Sarah Witzke wrote: Dear gromacs users, I would very much appreciate it if anyone could

[gmx-users] One more broken .trr file

Dear gromacs users, I would very much appreciate it if anyone could give me an advice on the following situation: I have run a simulation of a small molecule diffusion into a lipid membrane (gromacs version 4.0). The simulation was run for ~220 ns and stored in small individual .trr files

[gmx-users] One more broken .trr file

Dear gromacs users, I would very much appreciate it if anyone could give me an advice on the following situation: I have run a simulation of a small molecule diffusion into a lipid membrane (gromacs version 4.0). The simulation was run for ~220 ns and stored in small individual .trr files

RE: SV: SV: SV: [gmx-users] g_order version 4.0.x

happy now! Thanks again. -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Mon 09-03-2009 23:42 To: Gromacs Users' List Subject: Re: SV: SV: SV: [gmx-users] g_order version 4.0.x Justin A. Lemkul wrote: Sarah Witzke wrote: My .xtc file

SV: SV: [gmx-users] g_order version 4.0.x

, or do I have bad gromacs karma? Best regards and thank you, Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Sarah Witzke Sendt: ti 03-03-2009 11:37 Til: jalem...@vt.edu; Discussion list for GROMACS users Emne: SV: SV: [gmx-users] g_order version

SV: SV: SV: [gmx-users] g_order version 4.0.x

vegne af Justin A. Lemkul Sendt: ma 09-03-2009 22:38 Til: Discussion list for GROMACS users Emne: Re: SV: SV: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: Dear Justin and others, I have now tried the exact same command g_order command with the exact same result: /home/nat-mem

SV: SV: [gmx-users] g_order version 4.0.x

Good idea, I'll try that when I get home next week. -Sarah Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul Sendt: ma 02-03-2009 13:58 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] g_order version 4.0.x Sarah Witzke wrote

SV: [gmx-users] g_order version 4.0.x

Thank you David, I have filled a bugzilla. Fra: gmx-users-boun...@gromacs.org på vegne af David van der Spoel Sendt: ma 02-03-2009 10:55 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: Dear Gromacs users

[gmx-users] g_order version 4.0.x

Dear Gromacs users, I'm sorry to resend this email but I sent it yesterday (27 hours ago) and I still haven't received it myself. I'm sorry for the inconvenience it might cause. Sarah Dear Gromacs Users, I have simulated a lipid bilayer (128 DMPC

SV: [gmx-users] Grompp error in 4.x regarding dihedral multiplicity

of forces. Sarah Sarah Witzke wrote: Dear gromacs users, I'm doing simulations of small molecules in lipid bilayers. Doing the simulations with a DMPC bilayer works fine for all 4.x versions of gromacs. But when I try to do an energy minimization of a POPC bilayer, grompp gives

[gmx-users] Grompp error in 4.x regarding dihedral multiplicity

Dear gromacs users, I'm doing simulations of small molecules in lipid bilayers. Doing the simulations with a DMPC bilayer works fine for all 4.x versions of gromacs. But when I try to do an energy minimization of a POPC bilayer, grompp gives the following error: