[gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

Dear Gromacs users and Developers, I have performed dihedral PCA for 4 extracellular loops of a transmembrane protein after successfully finishing 100 ns of simulation at 300 and 310 K. I obtained figures for each loops for two different temperatures as in this link:

Re: [gmx-users] Solvating in a solvent other than water

Yes, I should have put up the images. I have uploaded two images, one of the expanded box before energy minimization and the other after, which shows the formation of blocks. I performed an NVT equilibration with this bad, 'block'ed box, and too many LINCS warning show up. 1. Before

[gmx-users] To calculate temperture in a specific region

Dear Gromacs users, I need to calculate temperature of molecules in a particular region after equilibration run (NVT or NPT) but during simulation molecules will exchange from one region to another. Can anyone have any suggestion in this regards ? Thanks. Krishna

Re: [gmx-users] addition of hydronium ion in simulation box

Thanks a lot...!!! Actually I was planning to do it with CPMD but I will also try the method suggested by you. On Tuesday, September 22, 2015, André Farias de Moura wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup!

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

Thank you Justin. I have to deduce some inference from this figure. Please make me out about the following queries. On Mon, Sep 21, 2015 at 5:48 PM, Justin Lemkul wrote: > > > On 9/21/15 4:00 AM, Naba wrote: > >> Dear Gromacs users and Developers, >> >> I have performed

[gmx-users] g_mmpbsa

Dear gromacs users, Can I use g_mmpbsa tool for calculation of binding free energy in RNA-ligand complex? Best, Leila Karami -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] To calculate temperture of the specific molecules after simulation.

Dear Gromacs users, I need to calculate temperature of molecules in a particular region after equilibration run (NVT or NPT) but during simulation molecules will exchange from one region to another. Can anyone have any suggestion in this regards ? Thanks. Krishna

Re: [gmx-users] addition of hydronium ion in simulation box

Hello justin, Thanks, actually I want to study movement of protons along the lenght of a water channel. Regards, Padmani On Monday, September 21, 2015, Justin Lemkul wrote: > [image: Boxbe] This message is eligible > for Automatic

Re: [gmx-users] Invalid order for directive atomtypes

So I have to make a single .itp file with the parameters of the solute and solvent? D.V. 2015-09-21 14:58 GMT+02:00 Justin Lemkul : > > > On 9/21/15 8:53 AM, Daniele Veclani wrote: > >> Dear Justin. >> >> Thanks for you quick answer, >> >> I checked the your suggested link. >>

Re: [gmx-users] Invalid order for directive atomtypes

On 9/21/15 9:07 AM, Daniele Veclani wrote: So I have to make a single .itp file with the parameters of the solute and solvent? You can approach it one of several ways (again, this is in the archive many times over), but all that matters is that any force field-level directive [*types]

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

On 9/21/15 4:00 AM, Naba wrote: Dear Gromacs users and Developers, I have performed dihedral PCA for 4 extracellular loops of a transmembrane protein after successfully finishing 100 ns of simulation at 300 and 310 K. I obtained figures for each loops for two different temperatures as in this

[gmx-users] Invalid order for directive atomtypes

Dear Gromacs Useres I'm trying to study a molecule in methanol (I have already studied this molecule in water) with charmm27 force field. I created the file .itp for methanol (solvent): [ atomtypes ] ; name at.num mass charge ptypesigmaepsilon CR 6 12.0110 0.0 A

Re: [gmx-users] Invalid order for directive atomtypes

Dear Justin. Thanks for you quick answer, I checked the your suggested link. But I have that both molecules (solvent and solute) introduce new atoms types. How can I do?? best regard D.V. 2015-09-21 14:15 GMT+02:00 Justin Lemkul : > > > On 9/21/15 8:06 AM, Daniele Veclani

[gmx-users] force fields selection

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 if anyone has experience with such system and why? appreciate any comments? I know

Re: [gmx-users] addition of hydronium ion in simulation box

for instance, take a look at this reference by Michele Parrinello to see some general remarks on how you should proceed if you really want to describe the dynamics of protons within a water channel: http://www.nature.com/nature/journal/v392/n6673/full/392258a0.html we have already done some

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

Sorry, I have posted my reply in wrong thread. On Tuesday, September 22, 2015, Padmani Sandhu wrote: > Hello justin, > > Thanks, actually I want to study movement of protons along the lenght of a > water channel. > > > Regards, > > > Padmani > > On Monday, September

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

Hello justin, Thanks, actually I want to study movement of protons along the lenght of a water channel. Regards, Padmani On Monday, September 21, 2015, Justin Lemkul wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup!

Re: [gmx-users] addition of hydronium ion in simulation box

It's not H3O+ that diffuses away, it is the H+ that moves from one molecule to the next instead. and protons behave quantum mechanically, so you should not expect any classical model to be able to properly describe their dynamics. for instance, you must consider that a proton may just tunnel

Re: [gmx-users] addition of hydronium ion in simulation box

On 9/21/15 9:49 PM, Padmani Sandhu wrote: Hello justin, Thanks, actually I want to study movement of protons along the lenght of a water channel. What you need is constant-pH MD, which is not natively supported in GROMACS. -Justin -- ==

Re: [gmx-users] simulating Cellulose using GAFF force field

Plot all energy components vs. time. Normally, the probem is within dihedrals, e.g. not all of them defined. On Mon, Sep 21, 2015 at 11:17 AM, Fahimeh wrote: > Hi gromacs users, > > I am trying to melt a crystalline structure of cellulose. This structure >

Re: [gmx-users] Prospective research areas of GROMACS

On 21/09/15 19:09, Sabyasachi Sahoo wrote: Dear Gromacs users and developers, I am a parallel programming researcher and would like to contribute to Gromacs molecular dynamics software by helping to nail down any bottlenecks that occur in scaling of the software on multiple CPUs (and probably

Re: [gmx-users] Prospective research areas of GROMACS

Thanks for the suggestion! On Mon, Sep 21, 2015 at 10:58 PM, David van der Spoel wrote: > On 21/09/15 19:09, Sabyasachi Sahoo wrote: > >> Dear Gromacs users and developers, >> >> I am a parallel programming researcher and would like to contribute to >> Gromacs molecular

[gmx-users] Prospective research areas of GROMACS

Dear Gromacs users and developers, I am a parallel programming researcher and would like to contribute to Gromacs molecular dynamics software by helping to nail down any bottlenecks that occur in scaling of the software on multiple CPUs (and probably improved performance in exa-scale era.) I am

Re: [gmx-users] Invalid order for directive atomtypes

On 9/21/15 8:53 AM, Daniele Veclani wrote: Dear Justin. Thanks for you quick answer, I checked the your suggested link. But I have that both molecules (solvent and solute) introduce new atoms types. How can I do?? Group them together and introduce them before any ligand [moleculetype]

[gmx-users] simulating Cellulose using GAFF force field

Hi gromacs users, I am trying to melt a crystalline structure of cellulose. This structure contains 8mers and monomers of cellulose molecules. To start the simulation, I computed the resp charges of 8mers and monomers of Cellulose and I am using GAFF force field for simulating this structure.

[gmx-users] addition of hydronium ion in simulation box

Hello all, How we can hydronium ions in a simulation box... With regards, Padmani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] g_mmpbsa

Dear gromacs users, Can I use g_mmpbsa tool for calculation of binding free energy in RNA-ligand complex? Best, Leila Karami -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Solvating in a solvent other than water

Possible the molecules are broken, but I've also seen this occur where the replica box (in this example evidently a 3x3x3 expansion) had slight gaps at the edge of the replicas, so when you minimise the energy, the clumps of matter pull themselves together. Try equilibrating under MD with a