Re: [gmx-users] Center to center distance in cylindrical micelles

You didn't give us much info about your system, so I will assume that your box is a rectangular prism and that all the cylinders are necessarily oriented along the z axis (e.g., because they are "infinite"/periodic). Since the center of mass (COM) of each cylinder must be a point on its axis, y

[gmx-users] Typo in table 3.1 of the reference manual?

Dear all, There is an inconsistency in the truncated octahedron entry in table 3.1 of the reference manual (version 2018 and all previous ones I checked). The value indicated for the bc and ab angles is 71.53 degrees, but the vectors a, b and c indicated in the table give the value 70.53 degre

Re: [gmx-users] Molecular Simulation using Ionic liquid

Hi Vidya, You should try to make your model "fit" into the existing forcefield you will be using. Also, you should validate the model with known physical properties (e.g., density, self-diffusion, shear viscosity, isothermal compressibility). It's usually difficult to get them all good, of cou

Re: [gmx-users] Calculation of nematic order parameter using gromacs

r' mean exactly? Nidhi On 30 May 2017 8:55 p.m., "Antonio Baptista" wrote: Hi Nidhi, If I remember correctly (and your use of "p2" suggests so), that should be the ensemble average of the 2nd-order Legendre polynomial of the angle between the molecular axis and the mem

Re: [gmx-users] How to calculate number of cholesterol molecules

On Thu, 1 Jun 2017, Justin Lemkul wrote: On 6/1/17 4:27 PM, Archana Sonawani-Jagtap wrote: Hi, I want to perform atomistic simulation in POPC bilayer with 30% cholesterol. So I want to know how to calculate number of cholesterol molecules for 30% concentration? Just for completion: it can

Re: [gmx-users] Calculation of nematic order parameter using gromacs

Hi Nidhi, If I remember correctly (and your use of "p2" suggests so), that should be the ensemble average of the 2nd-order Legendre polynomial of the angle between the molecular axis and the membrane normal, right? Although the order parameter computed by "gmx order" uses that same definitio

Re: [gmx-users] Order Parameter for HII phase

Hi Mohsen, I suggest you have a look at the QRB 1977 review by Seelig, that Tom already mentioned. Like for the planar case, they discuss how spectra of cylindrical lipid phases are related to the order parameter tensor (but I never looked into the details for that case). Anyway, I don't know

Re: [gmx-users] gmx gangle

Hi João, I used gangle to compute several angle distributions relative to the z-axis membrane normal, but that was almost a year ago, so I don't recall the details. But I can tell you that, after many failed attempts, I gave up from using fancy stuff in the -group1 and -group2 options. Instead

Re: [gmx-users] GROMOS 54a7 parameters for rare amino acids (eg. beta-alanine)

Hi Billy, I know that people from the University of Minho, Portugal, have parameterized several non-proteinogenic amino acids for GROMOS 54A7, making the parameters freely available. At least two papers are published: http://dx.doi.org/10.1021/jp4074587 http://dx.doi.org/10.1021/jp505400q Bu

Re: [gmx-users] PCA problems

On Wed, 8 Jun 2016, Tsjerk Wassenaar wrote: Hey :) That usually gives a fitted ensemble that more closely retains the original RMSD values between all pairs of structures. This should read: ... a fitted ensemble of which the sum of the traces of all pairwise inner product matrices is clo

Re: [gmx-users] PCA problems

Hi James, If your molecule shows some flexiblility, I would suggest using as a reference the structure of your original ensemble that produces the fitted ensemble with the lowest sum of RMSD values to that structure (or their square). That usually gives a fitted ensemble that more closely reta

Re: [gmx-users] Correct method to do Cartesian PCA

On Fri, 8 Jan 2016, Bin Liu wrote: Hi Tsjerk, I replicated their settings in their papers. The system size I used is larger than what they had. Could you elaborate on the reference used for fitting? Thank you so much. About the importance of the reference structure used for fitting in Cartes

Re: [gmx-users] force fields selection

On Tue, 22 Sep 2015, Justin Lemkul wrote: On 9/21/15 10:22 PM, James Lord wrote: Dear gmx users, I want to use either gromos 43a2 or 54a7 in Gromacs to simulate protein partitioning at biphasic liquid-liquid interfaces (Similar Justin's tutorial for biphasic system). Which one is recommended

Re: [gmx-users] Force-field bias???

On Wed, 5 Aug 2015, Justin Lemkul wrote: On 8/5/15 10:32 AM, Smith, Micholas D. wrote: OPLS-AA 2001 (the one implimented in gromacs) can be a little slow in folding (in both my experience, and from doi:10.1016/j.bpj.2009.04.061 ). That is not necessarily a bad thing if the peptide is suppo

Re: [gmx-users] definition of "eigenvector" in gromacs

Tsjerk, that's one of the coolest explanations of PCA I've ever read! :) Just one additional comment for Brett: Tsjerk's example assumes implicitly that your hands are actually moving parallel to the desk on average. On my desk, the meal is usually on top of the pile of papers that mysteriously

Re: [gmx-users] PCA projections using g_anaeig

Hi James, Yes, but all you need are the 1D projections, since they are the coordinates in the PCA reference frame. So, just combine them in any way you want, as Tsjerk indicated. Also, keep in mind that there is actually no transformation of the conformation space when you do PCA, just a rota

Re: [gmx-users] constant pH simulations in GROMACS 4.5

Hi, Our PB/MC/MD approach to constant-pH simulations is implemented up to version 4.0.7 of GROMACS, but we don't currently have a usable distribution -- after using some collaborators as guinea pigs, we came to the conclusion that the current implementation is unintelligible, since no one bes

Re: [gmx-users] Pressure Question

On Thu, 6 Nov 2014, Téletchéa Stéphane wrote: Le 06/11/2014 06:16, Antonio Baptista a écrit : In particular, the virial-based "instantaneous pressure" (call it P') computed in simulations has its ensemble average equal to the thermodynamic pressure P (check any good bo

Re: [gmx-users] Pressure Question

Well, it is definitely *not* "totally irrelevant to talk about pressure" when doing simulations in the NVT (canonical) or NVE (microcanonical) ensembles. Pressure, like temperature, volume, energy, numbers of particles, etc, is a thermodynamic property which is *always* defined for *any* system

Re: [gmx-users] Use NVT to mimic NVE

Then, run true NVE, for the reasons we already pointed. On Sat, 11 Oct 2014, Johnny Lu wrote: For dynamics with correct rate and correct fluctuation. On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban wrote: what is it needed for? Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Fri,

Re: [gmx-users] Use NVT to mimic NVE

On Fri, 10 Oct 2014, Mark Abraham wrote: On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote: Hi. Is it a good idea to mimic NVE by a NVT simulation with a large temperature coupling time constant, to reduce the effect of the thermostat ? Not if your observable is the total energy. But for m

Re: [gmx-users] Principal axes of inertia and g_principal

Hi Nicola, On Thu, 11 Sep 2014, nicola staffolani wrote: ​Dear GMX community, regarding the program g_principal and acknowledged the bug reported here ​ ​, I would like to understand what the meaning of the output of this pro

Re: [gmx-users] isothermal-isometric ensemble on gromacs

Well, the terminology is an old one, but not very common. An isometric ensemble is generally one in which the "extension" in the mechanical work term is kept constant. Thus, it may mean that the volume is kept constant in a volume/pressure system, that the area is kept constant in a area/surfac

Re: [gmx-users] Ion concentration of genion vs charmm-gui

Actually, your target concentration usually refers to the macroscopic solution bulk, not to the simulation box. Therefore, it is generally more correct to think in terms of the ion:solvent molar ratios -- that is, turn your molar concentration into the corresponding macroscopic ion:solvent mola

Re: [gmx-users] vdw radii in g_sas

You can indeed compute ff-dependent atomic radii from nonbonded parameters, which might be sometimes convenient (e.g., when trying to optimize a particular methodology). Some ways to do that are discussed in section 2.5 of http://dx.doi.org/10.1021/jp052259f. However, note that the surfaces, v

Re: [gmx-users] g_principal -- bug or very bad choice of filenames

Szilárd already activated it a couple of hours ago (just noticed he replied to me only). The issue is already submitted also. Thanks anyway. Best, Antonio On Wed, 19 Feb 2014, Mark Abraham wrote: It shows as active to me... Mark On Tue, Feb 18, 2014 at 11:46 PM, Antonio Baptista wrote

Re: [gmx-users] g_principal -- bug or very bad choice of filenames

On Fri, 7 Feb 2014, Justin Lemkul wrote: On 2/7/14, 6:08 PM, Antonio Baptista wrote: Dear all, This is a follow-up to an old thread on g_principal, which continues (as of version 4.6.5) to suffer from what I would call a bug or, at least, a very bad and misleading choice of output file

[gmx-users] g_principal -- bug or very bad choice of filenames

Dear all, This is a follow-up to an old thread on g_principal, which continues (as of version 4.6.5) to suffer from what I would call a bug or, at least, a very bad and misleading choice of output file names. This message is primarily a further warning to users, but I also hope that it promot