Re: [gmx-users] forcefields for lipids

/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe

Re: [gmx-users] forcefields for lipids

submitted, but for now have a look at this published paper: J. Phys. Chem. B, 2012, 116 (10), 3164-3179, doi: 10.1021/jp212503e All our parameters are available at on Lipidbook. Let me know if you need anything else! Best, J -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users

Re: [gmx-users] forcefields for lipids

:48 +0100 From: Thomas Piggot t.pig...@soton.ac.uk Subject: Re: [gmx-users] forcefields for lipids To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4fbb8b6c.70...@soton.ac.uk Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Joakim, I am interested to know what

Re: [gmx-users] forcefields for lipids

*From:* Thomas Piggot t.pig...@soton.ac.uk *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tuesday, May 22, 2012 7:39 PM *Subject:* Re: [gmx-users] forcefields for lipids Thanks Joakim, I will be very interested to see how these different lipids behave. This looks like

Re: [gmx-users] forcefields for lipids

suggest this forcefield for this kind of bilayer too? Thanks so much for your reply. Sincerely, Shima *From:* Thomas Piggot t.pig...@soton.ac.uk *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tuesday, May 22

[gmx-users] Lipid A Topology

group website (http://www.personal.soton.ac.uk/sk2x07/index.php), along with a structure file for this molecule. Cheers Tom Piggot -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] Re: dangling bond at at one of the terminal ends

and named as the force field expects them to be. You can't have anything missing or anything extra. Also, copying and pasting error messages directly from the terminal is vastly more helpful than a description. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users

Re: [gmx-users] Trajectories

mailto:er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] Berger lipid

interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text

Re: [gmx-users] Re: Gromacs 54a7 force field

of helical stabilization, from what I can see. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- 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

Re: [gmx-users] Re: Gromacs 54a7 force field

using combination rules (as for example done in the Berger/OPLS combination) is probably better. Cheers Tom On 19/07/12 00:15, Justin Lemkul wrote: On 7/18/12 6:57 PM, Thomas Piggot wrote: Hi, Justin, I am interested by your comments regarding the CHARMM lipids. In particular can you elaborate

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- 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

Re: [gmx-users] When to use Dispersion Correction for Lipid Bilayers

before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users

[gmx-users] ParmBSC0 Force Field Contribution

: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study Andrew T. Guy, Thomas J. Piggot, and Syma Khalid Biophysical Journal Volume 103, Issue 5, 5 September 2012, Pages 1028–1036 http://dx.doi.org/10.1016/j.bpj.2012.08.012 Cheers Tom -- Dr Thomas Piggot

Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer

dictate the velocities. I suppose if the run is stable enough, this is not a huge problem, but in general this combination is not recommended. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer

requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer

the mdp file I used is able to get more common APL and diffusion values even when averaging over a large number of simulations. As for the pressure in the x/y direction, is it more appropriate to use 1 atm or 0 atm for bilayer simulations? -David -- Dr Thomas Piggot University of Southampton, UK

[gmx-users] Reference for CHARMM36 Force Field Conversion

of the conversion for DPPC and POPC membrane systems (in terms of single point energies calculated in both GROMACS and NAMD) is provided in the supporting information of this work. Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Coordinate file for lipid bilayer

. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

Re: [gmx-users] Problem with equilibrated lipid bilayer structure

constraining all bonds (instead of just bonds to hydrogen atoms) with this force field. We found that we needed to increase the accuracy of the LINCS settings when constraining all bonds to ensure energy conservation. Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing

Re: [gmx-users] which version it is

15:42, 25 Sep 2012TomPiggot I am just wondering, is the the one with CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids? thank you very much best Albert -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] which version it is

: On 11/19/12 11:28 AM, Thomas Piggot wrote: Hi, As I understand it, the current and most up to date CHARMM protein force field (as included in both the charmm27 and charmm36 force field directories) is the CHARMM22 protein force field with the CMAP correction. In other words there would

Re: [gmx-users] which version it is

-- Message: 3 Date: Mon, 19 Nov 2012 16:28:28 + From: Thomas Piggot t.pig...@soton.ac.uk Subject: Re: [gmx-users] which version it is To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50aa5e2c.4000...@soton.ac.uk Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi

Re: [gmx-users] strange lincs warning with version 4.6

the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] source of opls Mg2+ parameters?

that are distributed with gromacs and verified that these c6/c12 values do not match the sigma/epsilon opls values after a conversion with g_sigeps. Thank you very much for your time and assistance, Chris. -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Parametrisation of the heteroatomic pdb

and compare with mdrun -rerun Rconfiguration.gro -s Lconfiguration. -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] forcefield.itp file for gromos45a3 and oplsaa

-- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests

Re: [gmx-users] Literature reading on DispCorr for energy and pressure

approximations it introduces and assumptions it makes. Section 4.8 of the manual gives many details, but I am curious if you can recommend any review-type articles about this correction. Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- Dr Thomas Piggot University

Re: [gmx-users] Ion parameters in OPLS AA force field

Jorgensen et al. from 2001. However I was not able to find the corresponding atom types in this article and so far also not in any other article of the OPLS-AA authors. Does anyone have an idea where these parameters come from ? /Flo -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users

Re: [gmx-users] Best Force Field for a Membrane Protein

...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] FWD:simulationg a distance restraint with a type 6 bond in gromacs

t.pig...@bristol.ac.uk University of Bristol, UK. -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un

Re: [gmx-users] decimal charge instead of integer

...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: [gmx-users] J-walking REMD

implementation of the method. Mark, you mentioned that you had coded an implementation Okur method (JCTC, 2006, 2, 420). How did it work and can you make this available? Any other thoughts on REMD for large systems are also appreciated. cheers David -- Thomas Piggot University of Bristol

Re: [gmx-users] H2 topology

-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] ATP for

, epsilon values etc. values. Where to get these values Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot t.pig...@bristol.ac.uk mailto:t.pig...@bristol.ac.uk wrote

Re: [gmx-users] Software inconsistency error: Not enough water

Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] Software inconsistency error: Not enough water

/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing

[gmx-users] Re: AMBER force fields for ATP

and epsilon values, or how to parametrize the P-OS-P bond. I was wondering, if you don't mind, could you point me in the right direction? Thanks very much, Alice Chang Liao Research Group Columbia University -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users

Re: [gmx-users] parametrization of FAD

or months) to just deriving suitable parameters. The piecemeal approach I describe for FAD seems to work pretty well, but may not always be possible or feasible. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Regards, Giulia Gonnelli -- Dr Thomas Piggot University

Re: [gmx-users] parametrization of FAD

I should also say that there are parameters for FADH(-) available for use with the amber forcefields: http://www.pharmacy.manchester.ac.uk/bryce/amber#cof Tom Thomas Piggot wrote: FAD has been prameterised previously. IIRC the parameters are in the appendix of the thesis of Anton Feenstra

[gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

tried using g_wham 4.0.7 but with exactly the same issues ,as well as using the pullf.xvg files as input to g_wham. I apologise if I am missing something obvious (or doing something silly!) but any help would be greatly appreciated. Cheers Tom -- Dr Thomas Piggot University of Southampton, UK

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

off, but I assumed that using -min and -max the -noauto option would have been the 'correct' way to do this. Cheers Tom Jochen Hub wrote: Thomas Piggot wrote: Hi, I am trying to construct a PMF profile for a phosphate ion passing through a membrane protein using umbrella sampling

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

pull_geometry=distance to get the complete PMF? Tom Jochen Hub wrote: Thomas Piggot wrote: Jochen thanks for your help. That was what I was afraid of you saying. Oh well, at least this will hopefully provide a useful reference so somebody doesn't make this same mistake. On a side note I noticed

Re: [gmx-users] PMF of ligand transport

/mailing_lists/users.php -- Aswathy -- Aswathy -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't

Re: [gmx-users] g_bundle issue

1991 [ bottom ] 2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132 2138 2146 Regards, Anirban -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] CG (MARTINI) parameters for RNA

MARTINI force field? All the best, Itamar -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe

Re: [gmx-users] How to use Inflategro with different lipid types

this procedure so the lipids do not simply slam into one another and distort the membrane. Once you've achieved a reasonable membrane, solvate and equilibrate for a longer period of time in the presence of solvent and absence of any restraints. -Justin Kindest regards, Yiannis -- Dr Thomas Piggot

Re: [gmx-users] lipids per area charmm36 popc

membranes. Lipid rotational relaxation is on the order of 5 ns, and translational relaxation about 10 ns. I'd say you need at least 20 ns of simulation to make any real conclusions, with some of that of course discarded as equilibration. -Justin -- Dr Thomas Piggot University of Southampton

Re: AW: Re: [gmx-users] where can I download POPC membrane file?

. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Calculation of unsaturated deuterium order parameters for POPC

Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

0.0738068 -0.000533683 that you should then replace in the correct positions in the sn2 output good luck, and sorry if i'm missing the point :| igor Igor Marques On Wed, Jun 8, 2011 at 5:53 PM, Thomas Piggot t.pig...@soton.ac.uk mailto:t.pig

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

to calculate the order parameters from the all-atom CHARMM36 simulations using a different bit of code, I will report back with the results if we can get this to work. Cheers Tom Justin A. Lemkul wrote: Thomas Piggot wrote: Hi Igor, Thanks for the reply but I think you slightly missed the point I

Re: [gmx-users] All-atom topologies for lipid head groups

really want an AA representation of your molecules, you're probably better off just applying the CHARMM force field to the whole system. The latest version of Gromacs supports CHARMM, which includes a number of common lipids. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

an issue regarding this on redmine. Cheers Tom Thomas Piggot wrote: Hi, Both the trajectories are 100 ns in length (plus I have a repeat of each simulation using different starting velocities). The results from a block analysis, and analysis of the repeat simulations, give almost identical

Re: [gmx-users] Charge groups in Charmm for lipids

. Was this changed on purpose? The beta version seems correct to me, but am I missing something as to why this change would be made? Thanks -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] Charge groups in Charmm for lipids

Sure, I will upload a GROMACS 4.5.4 version of the force field files to the website. Cheers Tom On 06/08/11 01:34, Peter C. Lai wrote: On 2011-08-05 06:48:09PM -0500, Thomas Piggot wrote: Hi, Yes, this was done on purpose to reflect the different use of charge groups in CHARMM and GROMACS

Re: [gmx-users] Charge groups in Charmm for lipids

. Sorry for any problems caused by this. Cheers Tom On 06/08/11 02:28, Thomas Piggot wrote: Sure, I will upload a GROMACS 4.5.4 version of the force field files to the website. Cheers Tom On 06/08/11 01:34, Peter C. Lai wrote: On 2011-08-05 06:48:09PM -0500, Thomas Piggot wrote: Hi, Yes

Re: [gmx-users] Error from residues added to rtp file

on the origin of this error, and on what I can do to correct it. I am using Gromacs 4.5.3. Thanks a lot in advance, Antoine -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] MARTINI / all-atom mapping

-- Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison) -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users

Re: [gmx-users] CHARMM36 force field

? Best regards Giovanni -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un

Re: [gmx-users] CHARMM 36 force field

with the NPT ensemble, may I have access to it? Best regards Giovanni -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] topologies for POPE and DMPE

and DMPE. Anybody knows where can i get the topologies file for POPE and DMPE ? Any help is much appreciated. Thanks a lot! Roy -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] topologies for POPE and DMPE

bilayer. Do, you have POPC structure and itp files parameterised by CHARMM 27 FF. Regards, Pramod On Mon, Oct 17, 2011 at 12:07 PM, Thomas Piggot t.pig...@soton.ac.uk wrote: Hi Roy, PE lipids are less frequently used than PC ones and there are fewer topologies available. Also it has been shown

Re: [gmx-users] Charmm27 ff for membrane protein simulation

is necessary. Run pdb2gmx on a single lipid molecule, convert the .top to .itp (see the wiki) and #include it in the .top for your protein, just like in my tutorial. -Justin Thank you for help James -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users

Re: [gmx-users] OPLS-AA topologies for ATP

post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx

Re: [gmx-users] OPLS-AA topologies for ATP

? Is it more compatible with OPLS? Thanks, Bin On Jun 23, 2010, at 2:48 AM, Thomas Piggot wrote: Well I would suggest you should do some very careful testing to validate the combination of CHARMM charges and one dihedral with the rest of the parameters from OPLS. It is not very common (or generally wise

Re: [gmx-users] deletion of some water molecules

environment of pr-dna complex and not water molecules being in edges or rest of box. Is there any way to do that? -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] Nucleotides for charmm port

it in stream file and have no idea how to convert it. It should be possible (for someone smarter than me). cheers Dave -- Dr Thomas Piggot University of Southampton, UK. [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper

Re: [gmx-users] ARG Charmm gmx 4.5.1

-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] Problem with pdb2gmx and a new residue

://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx

Re: [gmx-users] Issue with Atom Types/Charges/Mass when including ATP in gromos53.a6

! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] charmm c36 lipids

it to me. I am trying to use the new CHARMM36 lipids for a simulation with a membrane protein. Thank-you. Drew Bennett -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: [gmx-users] cholesterol

posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] charmm c36 lipids

is the same and report back to the list. I don't see anything which would not work for your script as there are not any major changes to the forcefield in CHARMM36. -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] CHARMM36 Force Field

the conversion by Par Bjelkmar without any differences seen and allow the simulation of membrane protein systems. If anyone has any questions (or thinks they have found any mistakes!) then feel free to contact me (which is probably best done through the mailing list). Cheers Tom Piggot -- Dr Thomas

Re: [gmx-users] CHARMM36 lipid bilayers

in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results

Re: [gmx-users] CHARMM36 lipid bilayers

get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files

Re: [gmx-users] CHARMM36 lipid bilayers

with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot

Re: [gmx-users] Gromos 45A4

-- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests

Re: [gmx-users] who has the force field file of gromos45a4

://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx

Re: [gmx-users] New release: 4.5.2

simulating! Rossen -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un

[gmx-users] Re: Charmm36 FF and membrane

. Best regards. -- Dr. Tusar Bandyopadhyay Theoretical Chemistry Section, Chemistry Group BARC, Trombay Mumbai 400 085 INDIA Tel: 022-2559 0300 email: tusaratb...@gmail.com mailto:tusaratb...@gmail.com -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users

[gmx-users] Re: Charmm36 FF and membrane

small (by XY dimension) for my purpose. I am still trying with Charmm36 FF. Regards On Mon, Nov 1, 2010 at 4:21 PM, Thomas Piggot t.pig...@soton.ac.uk mailto:t.pig...@soton.ac.uk wrote: Hi, This is more of a GROMACS problem than a specific problem related to this lipid conversion

Re: [gmx-users] Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?

-463287 24955.755 -165.768 (kJ/mol) I am particularly eager to obtain from you some comments and advices about these findings. Thanks you so much for your help. SA -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Re: gmx-users Digest, Vol 79, Issue 167

-165.498 (kJ/mol) Total Energy-463287 24955.755 -165.768 (kJ/mol) I am particularly eager to obtain from you some comments and advices about these findings. Thanks you so much for your help. SA -- Dr Thomas Piggot

[gmx-users] Fwd: lateral diffusion coefficients on a spherical surface

Hi, I am forwarding on a message on behalf of one of my colleagues who is having problems sending messages to the list. Please take a look his message and see if you can help him with his problem. Thank you Tom Piggot Original Message Subject:lateral diffusion

Re: [gmx-users] dna, lipid simulation

| Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu mailto:itamar.k...@monash.edu -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] CMAP error

-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] Re:Re: Which FF could be used for protein-RNA MD simulation in GROMACS?

with the G53a6 FF. Aside from that though, I don't remember which lab/site had them. The same is true for lipid and carbohydrate .itp/.rtp libraries. Stephan Watkins -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] galactose bond stretch

I have added an issue on redmine. Cheers Tom Justin A. Lemkul wrote: Thomas Piggot wrote: Whilst this 'problem' you are seeing is probably as Justin has described (a periodic boundary visualisation effect), you should also beware when performing carbohydrate/sugar simulations

Re: [gmx-users] N-acetyl-d-glucosamine parameters

be appreciated, Thanks Renato -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post

Re: [gmx-users] grompp charge group radii larger than rlist

as to what causes this problem? Much obliged for your help. Cheers, Ramon -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] Re: change in the secondary structure after simulation

the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University

Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

, I don't know whether charges missing from a [moleculetype] definition are looked up in ffnonbonded.itp. Mark -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: [gmx-users] Calculating diffusion coefficient in three dimension

://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting