[gmx-users] Question regarding g_order

2013-10-03 Thread sa
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 las

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

2013-06-15 Thread sa
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] How to compute the C-H bond time correlation function for surfactant alkyl chain in micelle with the CHARMM and GROMOS

2012-07-18 Thread sa
n chain backbone. Again 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/Suppo

[gmx-users] Question about the translational diffusion

2012-07-05 Thread sa
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] Conversion of the GLYCAM dihedral parameters

2011-08-08 Thread sa
> > Thank you Olivier for your response. > SA > -- > > Message: 2 > Date: Thu, 28 Jul 2011 11:20:44 +0100 > From: Oliver Grant > Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters > To: Discussion list f

[gmx-users] Conversion of the GLYCAM dihedral parameters

2011-07-21 Thread sa
> > 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: &qu

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

2011-07-20 Thread sa
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" > S

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

2011-07-19 Thread sa
0.0-3. 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/listinf

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

2011-06-28 Thread sa
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 con

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

2011-06-25 Thread sa
5 # Totals60246010 # SS %0.64 0.26 0.64 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] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC

2011-04-10 Thread sa
Thank you David A bientôt SA > -- > > Message: 1 > Date: Sun, 10 Apr 2011 11:17:15 +0200 > From: David van der Spoel > Subject: Re: [gmx-users] Different g_sas values between AMBER, CHARMM >and

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

2011-04-10 Thread sa
the carbon 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

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

2011-04-09 Thread sa
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 the

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

2011-03-29 Thread sa
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 > Fro

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

2011-03-28 Thread sa
atom with itself, 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

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

2011-03-28 Thread sa
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 > - next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users

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

2011-03-28 Thread sa
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 > Thank

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

2011-03-28 Thread sa
Buckingham: 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, > > > &

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

2011-03-27 Thread sa
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 se

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

2011-03-16 Thread sa
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. &g

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

2011-03-16 Thread sa
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 i

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

2011-03-16 Thread sa
rrors --- 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

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

2011-03-16 Thread sa
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 paramet

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

2011-03-14 Thread sa
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 m

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

2011-03-07 Thread sa
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 ? > > >

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

2011-03-07 Thread sa
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

[gmx-users] Dihedral angles distribution

2011-03-07 Thread sa
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] How to obtain the average radial density functions relative to the center of mass with g_rdf.

2011-02-28 Thread sa
0.9 g/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

[gmx-users] Values of radial density profiles

2011-02-25 Thread sa
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] g_sas values for peptide in water and in DPC micelle

2011-01-03 Thread sa
the accessible surface area with respect to solvent for some residues of the peptide and especially for the single TRP of the peptide (TRP553) and compare with the SA obtained for the same peptide in water. By examining several configurations of the peptide in the B system at the end of the

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

2010-12-09 Thread sa
ted 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 h

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

2010-12-05 Thread sa
version and finally how the charge group distribution to compute the force during the simulations. http://hpics.li/9ed5ee1 --> 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

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

2010-11-26 Thread sa
ere there are more terms). =-O To be sure that this difference has no impact in the MD, i going to do other MD. I will come back soon. Thanks you again SA > > Cheers > > Tom > > On 25/11/10 22:42, sa wrote: > > Dear All, > > > > In a previous message &g

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

2010-11-25 Thread sa
-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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Ple

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

2010-11-14 Thread sa
that chargegrp "yes" option should not be used in MD 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://l

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

2010-11-12 Thread sa
> > > 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 with

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

2010-11-12 Thread sa
> 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] g_densmap options and use

2010-11-12 Thread sa
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 the

[gmx-users] Problems with NVT simulation with CHARMM27

2010-10-21 Thread sa
r 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 before posting! Please don't post (un)subscribe requests to the list. Use the www interface