Re: [gmx-users] (no subject)

This usually means that your system is not well equilibrated. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Wed, Oct 15, 2014 at 6:13 AM, Padmani Sandhu wrote: > Hello, > > > I am doing Molecular-Dynamic simulation of Protein-Ligand complex embedded > in POPC lipid membrane. After energy

Re: [gmx-users] 2-D liquid

I believe 2D liquid is a liquid film. If so, none of your options will work. You need to surround the liquid film with a layer of vacuum and simulate NVE ensemble. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Wed, Oct 15, 2014 at 6:06 AM, Cai wrote: > Hi users, > > I am trying to simulat

Re: [gmx-users] 2-D liquid

On 15.10.2014 06:06, Cai wrote: I am trying to simulate 2-d liquids interacting with simple potential like Lennard-Jones potential. Can it be done by specifying "pcoupletype = semiisotropic" in the .mdp file? I mean enforcing a normal pressure in x-y direction while very high pressure in z direct

[gmx-users] Fwd: Running free energy tutorial for ionic molecules

Dear Users, I am resending this mail, as I am still stuck with the error. Now I have upgraded my Gromacs from version-4.5.5. to version-5.0.2, I am able to run the simulation using Gromacs-5.0.2 for sytems with 1-octanol as solvent, whereas the system with water as solvent is still giving errors wi

[gmx-users] retaining the active site water molecules in the protein -reg

hello In my task some water molecules in one protein active site and it playing one of the role of interactions and binding affinity if i want retain that water molecules in active site to preform the simulations what i want to do ? further -- Regards, S.VENKATESH, -- Gromacs Users mailing lis

Re: [gmx-users] regarding confout.gro

hello justin i have been visualized the file of confout.gro file in vmd and the position of protein and ligand is ok i know i have to analyze all the parameters like energy and rmsd is it sufficient to extend my simulation or which file i have to visualized On Tue, Oct 14, 2014 at 5:25 PM, Justin

[gmx-users] CAKot8D6knnhu1_vHLDfCzF-_Zsw+85jScMbho=st6qg3p3j...@mail.gmail.com

Hello I have energy minimized the complex successfully and I dont understand whats wrong with the system. -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin 176206, Di

Re: [gmx-users] Velocity Verlet integrator

Dear all, I am still interested in some integrator related issues. I understand that the easiest way to implement velocity Verlet was to split the updates in two updates. But I don't understad the order of those updates. I mean why there are two updates for velocities and then the update for posi

Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?

On 10/14/14 11:37 PM, Batdorj Batsaikhan wrote: Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? How is it that you're attempting to calculate this quantity? -Justin -- ===

Re: [gmx-users] Unstable system [was: (no subject)]

Please remember to use a sensible subject line. On 10/15/14 6:53 AM, Padmani Sandhu wrote: Hello I have energy minimized the complex successfully and I dont understand whats wrong with the system. What were Epot and Fmax from minimization? Please copy and paste the actual output. What f

Re: [gmx-users] regarding confout.gro

On 10/15/14 6:25 AM, RINU KHATTRI wrote: hello justin i have been visualized the file of confout.gro file in vmd and the position of protein and ligand is ok i know i have to analyze all the parameters like energy and rmsd is it sufficient to extend my simulation or which file i have to visuali

Re: [gmx-users] retaining the active site water molecules in the protein -reg

On 10/15/14 5:06 AM, venkatesh s wrote: hello In my task some water molecules in one protein active site and it playing one of the role of interactions and binding affinity if i want retain that water molecules in active site to preform the simulations what i want to do ? further Simply ret

Re: [gmx-users] Velocity Verlet integrator

On 10/15/14 7:30 AM, Mario Fernández Pendás wrote: Dear all, I am still interested in some integrator related issues. I understand that the easiest way to implement velocity Verlet was to split the updates in two updates. But I don't understad the order of those updates. I mean why there are

Re: [gmx-users] Velocity Verlet integrator

Yes, I understand that. But my question is more about why the two velocity updates are implemented before the position update and not the other way round? From the theoretical point of view I would think more in one of the following schemes: 1. Calculate: [image: \vec{v}\left(t + \tfrac12\,\D

Re: [gmx-users] Velocity Verlet integrator

Because the 'start' of the vv integrator step is halfway through the loop. This is a byproduct of 1) putting leapfrog and velocity verlet in the same loop and 2) minimizing communication and output. It is not as elegant as it should be. There are efforts to clean this up, but it's a lot of reorga

Re: [gmx-users] Velocity Verlet integrator

Thank you very much Professor Shirts. I have these doubts because I am trying to implement new integrators based in the concatenation of two VV steps to make a single step. The idea follows the integrators suggested in http://web.mit.edu/~ripper/www/research/efficient_md_integrators.pdf This is w

Re: [gmx-users] Velocity Verlet integrator

Yes, I've been using the theory here: http://arxiv.org/abs/1301.3800 Which describes how to concantenate integrator steps in a formal way. I can say that the time savings you get by concatenating integrators is VERY small. The only time it is nonnegligible is when there is a LOT of communicatio

[gmx-users] how to build topology

Hello everybody, I want to build a topology for a lipid to use the parameters reported by Jämbeck and Lyubartsev Jämbeck, Joakim P. M., y Alexander P. Lyubartsev. «Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids». J. Phys. Chem. B 116, n.o 10

Re: [gmx-users] Velocity Verlet integrator

Thank you very much for this reference. I will take a look at it carefully. We are trying to develop and implement this integrators for hybrid Monte Carlo simulations and our interest is not really related to time saving but to sampling efficiency. Right now it doesn't look straightforward to me

Re: [gmx-users] Unstable system [was: (no subject)]

Hello Justin, Epot = -3.4264112e+07 Fmax= 8.5767386e+02 from energy minimization. I am using force field Gromos43a1 and ligand parameters were derived from PRODRG. I have also minimized same protein-ligand complex in the water ealier. Regards, Padmani On Wed, Oct 15, 2014 at 5:05 PM, Justin

[gmx-users] How to add iron parameter?

Hi, I’m a beginner of gromacs. I want to do simulation for a protein with protein with ferrous or ferric. But there is no iron in force field. What is easiest way to do it? Can I just add a few lines to aminocids.rtp, like this? [FE] [ atoms] FE FE3.0 [ bonds] [ angles ]

[gmx-users] g_dist as an alternative for g_saltbr

Fellow users,I have read several emails exchanged in this discussion list where g_dist is presented as a better choice for observing salt bridges in the trajectory. And I'm totally inclined to agree with that, but that would be the case where you already know which are the SBs present in the system

Re: [gmx-users] How to add iron parameter?

Pure md doesn't deal with complex orbitals well, I guess. Hydrogen bonds in pure md is not directional, as it should be. can molecular dynamics (md) simulate heavy metals, like iron, which have d oribtals? I heard that even calcium is a bit troublesome in md. On Wed, Oct 15, 2014 at 1:22 PM, Gua

[gmx-users] g_dist as an alternative for g_saltbr

Fellow users, I have read several emails exchanged in this discussion list where g_dist is presented as a better choice for observing salt bridges in the trajectory. And I'm totally inclined to agree with that, but that would be the case where you already know which are the SBs present in the sys

Re: [gmx-users] How to add iron parameter?

not sure if this helps. But maillist once mentioned parameter for heme (that are not necessary good): http://comments.gmane.org/gmane.science.biology.gromacs.user/59978 http://ccl.net/chemistry/resources/messages/2008/09/22.001-dir/index.html https://www.mail-archive.com/gmx-users@gromacs.org/msg2

Re: [gmx-users] How to add iron parameter?

"The easiest way" is to simulate QM/MM around Fe (+howmuch?). Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Wed, Oct 15, 2014 at 7:22 PM, Guangyu Zhu wrote: > Hi, I’m a beginner of gromacs. I want to do simulation for a protein with > protein with ferrous or ferric. But there is no iron

Re: [gmx-users] how to build topology

I believe only writing the ITP file(s) by hand. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Wed, Oct 15, 2014 at 5:49 PM, Victor Rosas Garcia wrote: > Hello everybody, > > I want to build a topology for a lipid to use the parameters reported > by Jämbeck and Lyubartsev > > Jämbeck, Joaki

Re: [gmx-users] How to add iron parameter?

On 10/15/14 2:05 PM, Johnny Lu wrote: Pure md doesn't deal with complex orbitals well, I guess. Hydrogen bonds in pure md is not directional, as it should be. can molecular dynamics (md) simulate heavy metals, like iron, which have d oribtals? I heard that even calcium is a bit troublesome in

Re: [gmx-users] Unstable system [was: (no subject)]

On 10/15/14 12:35 PM, Padmani Sandhu wrote: Hello Justin, Epot = -3.4264112e+07 Fmax= 8.5767386e+02 from energy minimization. Seems reasonable. I am using force field Gromos43a1 and ligand parameters were derived from PRODRG. PRODRG produces topologies full of errors. Have you done a

Re: [gmx-users] g_dist as an alternative for g_saltbr

On 10/15/14 2:19 PM, Diogo Martins de Sá wrote: Fellow users, I have read several emails exchanged in this discussion list where g_dist is presented as a better choice for observing salt bridges in the trajectory. And I'm totally inclined to agree with that, but that would be the case where y

Re: [gmx-users] how to build topology

darn it! I was hoping the answer would be different. :( Perhaps I can take the topology from acpype and tweak the atomtypes by hand. Are there any caveats or potential traps in doing this? Victor 2014-10-15 15:13 GMT-05:00 Dr. Vitaly Chaban : > I believe only writing the ITP file(s) by hand. >

Re: [gmx-users] how to build topology

On 10/15/14 4:40 PM, Victor Rosas Garcia wrote: darn it! I was hoping the answer would be different. :( Perhaps I can take the topology from acpype and tweak the atomtypes by hand. Are there any caveats or potential traps in doing this? The authors provide the entire Gromacs-compatible for

Re: [gmx-users] how to build topology

but... the lipids I am interested in are not included in the files provided by the authors. I want to make a new lipid that is compatible with said forcefield. Victor 2014-10-15 15:46 GMT-05:00 Justin Lemkul : > > > On 10/15/14 4:40 PM, Victor Rosas Garcia wrote: >> >> darn it! I was hoping the

Re: [gmx-users] how to build topology

On 10/15/14 5:11 PM, Victor Rosas Garcia wrote: but... the lipids I am interested in are not included in the files provided by the authors. I want to make a new lipid that is compatible with said forcefield. I see no advantage in trying to use acpype or any other tool, just to change the en

Re: [gmx-users] how to build topology

OK, I'll try that. thanks for your input Victor 2014-10-15 16:28 GMT-05:00 Justin Lemkul : > > > On 10/15/14 5:11 PM, Victor Rosas Garcia wrote: >> >> but... the lipids I am interested in are not included in the files >> provided by the authors. I want to make a new lipid that is compatible >> w

Re: [gmx-users] Fwd: Running free energy tutorial for ionic molecules

Which bonds are rotating too far? At what lambda values and which decoupling process is this occurring? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu

Re: [gmx-users] Unstable system [was: (no subject)]

I have also carried out MD simulation for the same comlex in water and that worked perfectly. On Thu, Oct 16, 2014 at 1:50 AM, Justin Lemkul wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule >

Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?

I want to calculate free energy of 2 different types of 71 amino acids long protein. I run General Equilibration (NPT). Then I run free energy calculation of 200 ps. When calculation start, I got following warming message: ** WARNING: Listed nonbonded interact