[gmx-users] Question about the translational diffusion

Hi all, : A quick question here: Does the g_msd program (v4.5.5) take into account the finite size effect due to PBC when it computes/gives translational diffusion ? sa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text

[gmx-users] How to compute the C-H bond time correlation function for surfactant alkyl chain in micelle with the CHARMM and GROMOS

how to do that ? Your guidance would be helpful for me. Best SA -- 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://www.gromacs.org/Support/Mailing_Lists

[gmx-users] About the %SS values in the output of do_dssp

0.11 I can understand how the %SS values are obtained in the example given in http://redmine.gromacs.org/issues/683, but not in my case. Could you tell me how the %SS is obtained the output above. Thank you in advance for your help SA -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Re: About the %SS values in the output of do_dssp

Ok Thank you Justin for this clarification sa wrote: Dear All, I have simulated 6 peptides (with 7 AA each capped in N and C termini) in water and trehalose. During all the simulation time, the six peptides have b-sheet conformations. I would like to calculate the average

[gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format.

-3. Dimethyl phosphate 1 -0.50 0.0-2. 10.10 0.0 1 Thank you in advance, for your help SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format.

that in the AMBER ff port in GROMACS, the multiplicity values are always set to 0 and the barrier heights have sometime a negative value. Thank you again for your advice. SA- Message: 1 Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT) From: Austin B. Yongye ybau...@yahoo.com Subject: Re: [gmx

[gmx-users] Conversion of the GLYCAM dihedral parameters

Yeah I have also found this page. Finally I did the conversion. I am currently testing the parameters. Thank you Austin and Mark for your help SA- -- Message: 4 Date: Wed, 20 Jul 2011 07:17:18 -0700 (PDT) From: Austin B. Yongye ybau...@yahoo.com Subject

[gmx-users] Conversion of the GLYCAM dihedral parameters

Thank you Olivier for your response. SA -- Message: 2 Date: Thu, 28 Jul 2011 11:20:44 +0100 From: Oliver Grant olivercgr...@gmail.com Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters To: Discussion list for GROMACS users gmx-users

[gmx-users] Problems with NVT simulation with CHARMM27

help. sa -- 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 to the list. Use the www interface or send

[gmx-users] g_densmap options and use

Dear All, I would like to compute the average 2D density distribution of the water around 6 peptides aggregated in the cluster within the simulation box with gromacs, for that I think that g_densmap is the the good tool (correct ?). However it is not very clear for how to use g_densmap. Below

[gmx-users] Re: gmx-users Digest, Vol 79, Issue 88

On 13/11/2010 4:07 AM, sa wrote: Dear All, I would like to compute the average 2D density distribution of the water around 6 peptides aggregated in the cluster within the simulation box with gromacs, for that I think that g_densmap is the the good tool (correct ?). However

[gmx-users] Re: gmx-users Digest, Vol 79, Issue 89

sa wrote: On 13/11/2010 4:07 AM, sa wrote: Dear All, I would like to compute the average 2D density distribution of the water around 6 peptides aggregated in the cluster within the simulation box with gromacs, for that I think that g_densmap

[gmx-users] Spurious results with pdb2gmx -chargegrp yes option

with CHARMM force field in GROMACS, as it was discussed recently in this mailing list (for example http://lists.gromacs.org/pipermail/gmx-users/2010-September/054106.html). SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

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

) I am particularly eager to obtain from you some comments and advices about these findings. Thanks you so much for your help. SA -- 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

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

will come back soon. Thanks you again SA Cheers Tom On 25/11/10 22:42, sa wrote: Dear All, In a previous message (http://lists.gromacs.org/pipermail/gmx-users/2010-November/055839.html ), I described the results obtained with MD performed with the CHARMM27 ff and the chargegrp

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

-- Secondary structure vs. time http://hpics.li/7cf1625 -- RMSD vs. time So i suspect that the errors come from the use a bad version of the CHARMM27 ff Thank you all for your preceding comments SA Francesco Oteri wrote: To see if the problem is force-field related, you could try to run

[gmx-users] How to obtain the semi-axis lengths from inertia tensor for an aggregate

in the mailing list few days ago, unfortunately no response was given: http://www.mail-archive.com/gmx-users@gromacs.org/msg35963.html Thanks in advance SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Values of radial density profiles

and 16.4 ). What is wrong with command used above. Did i forget something ? Thank you in advance for your help. SA -- 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

[gmx-users] How to obtain the average radial density functions relative to the center of mass with g_rdf.

/cm3. Did i compute the expected function with above command ? If not, how to obtain the rdf (in g/cm3) for each components ? Thanks for the help. SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Dihedral angles distribution

in the middle of the alkyl chain, i obtain an average value 0° (!!) and the following figure http://www.hostingpics.net/viewer.php?id=825755angdist.png This is not what i expect How to obtain simply the classical normalized function from g_angle ? Thank you in advance for your advices SA -- gmx-users

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 40

Yes justin, the average is not 0 but around 0° (0.584577). But how to obtain the Average normalized dihedral distribution for example this dihedral? is few words the figure with g_angle ? http://cmt.dur.ac.uk/sjc/thesis_dlc/node106.html Thank you again sa wrote: Dear GMXusers I

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 41

OK, i will try your suggestion. Thank you SA sa wrote: Yes justin, the average is not 0 but around 0° (0.584577). But how to obtain the Average normalized dihedral distribution for example this dihedral? is few words the figure with g_angle ? http://cmt.dur.ac.uk/sjc/thesis_dlc

[gmx-users] g_order for DPC alkyl chain in the micelle

Dear all, I would like to compute the order parameter tensor elements of a DPC micelle with respect to a vector direction (for example the vector from the center of mass of the micelle to the phosphorus atom). It is possible with g_order (4.5.3). if yes how ? Thank you in advance. -- gmx-users

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 106

Thank you Angel, I will try your suggestion. Cheers SA Hi very recently I faced the same problem with a system that gives micelles of different geometries and, as far as I saw, g_order don't do that. Then I decided to compute a kind of local order parameters defined as: S_i=(3 cos

[gmx-users] g_order for DPC alkyl chain in the micelle

--- Did I make a error, what is the correct approach. to obtain the angle between 2 vectors ? Thank you in advance SA -- Message: 3 Date: Wed, 16 Mar 2011 10:06:44 +0100 From: ?ngel Pi?eiro angel.pine...@usc.es

[gmx-users] Re: g_order for DPC alkyl chain in the micelle

Ok Justin, So which gmx tool i can use to obtain the angle between two vectors defined by two atom pairs ? SA sa wrote: Hi all This message is related with my previous message (see below) about the calculation of the order value for the DPC alkyl chain in a micelle. So if I

[gmx-users] g_order for DPC alkyl chain in the micelle

OK Angel, I will contact you off-list SA Dear SA To be honest I am not sure this can be done by using g_angle, I used my own code for this calculation. I could send it to you if you send me a message off the list... but I would prefer to talk with a non-anonymous. Cheers, Ã ngel

[gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

help. SA -- 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 to the list. Use the www interface or send

[gmx-users] mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

: A = 199065, B = 34.0796, C = 0.00466239 Back Off! I just backed up potje.xvg to ./#potje.xvg.8# gcq#342: Ich war schwanger, mir gings zum kotzen (Nina Hagen) Did I miss something ? Thank you again for your help SA sa wrote: Dear All, I would like to compute the C6 and C12 LJ terms

[gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

Sorry I forget to say in my previous mail that the values obtained by g_sigeps_mpi are not similar to the values given in the GROMOS53A6 ffnonbonded.itp for the OM atom. OM8 0.000 0.000 A 0.0022619536 7.4149321e-07 So your advices are welcome. SA 2011/3/28 sa sagmx.m

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 196

Thank you Justin, It is good to know i am not alone to not understand. So I will ask to the authors the reason of this discrepancy. Bye SA 2011/3/28 gmx-users-requ...@gromacs.org - next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx

Re: [gmx-users] Re: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

, correct ? And the nonbond_types section, the comb-rules with the other atoms types. So if I take into account only the OM atom, as an example, why I obtained different values for C6 and C12 terms in the [ atomtypes ] section. Thank you again for your help. SA

[gmx-users] RE: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

Dear All, Finally, I resolved my problem by contacting the author of the paper (thanks to D. Poger). They gave me the correct value for the epsilon and sigma (0.2137 nm instead of 0.3137 nm in the paper). SA Message: 2 Date: Tue, 29 Mar 2011 09:45:34 +1100 From: Mark Abraham mark.abra

[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC

from the correct mass and radius of the atom type. WARNING: could not find a Van der Waals radius for 54 atoms It is important ? Thank you in advance for your advices. SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC

atoms (including the headgroup carbon atoms). Thank you SA On 2011-04-09 19.06, sa wrote: Dear All, I have simulated three DPC micelles with the same size (54 lipids) with different force fields (CHARMM, AMBER et GROMOS53A6) and computed the average accessible surface areas for each

[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC

Thank you David A bientôt SA -- Message: 1 Date: Sun, 10 Apr 2011 11:17:15 +0200 From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Different g_sas values between AMBER, CHARMM

[gmx-users] Problems with simulations of a triclinic crystal lattice with Parrinello-Rahman

93.50 110.06 P 1 Did I miss something important here about PR and crystals? SA -- 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

[gmx-users] Question regarding g_order

Hi all, I am trying to compute the order parameters for the sn1 and sn2 chains of DOPC (CHARMM36) in bilayer . I am using the g_order tool (v4.6.3). I have constructed for each DOPC chain two index files that contains in the first one all the Carbon atoms where the first Carbon is C=O and the