Re: [gmx-users] Temperature or Pressure Coupling

Thank You Sir. I have another question? What should be the ideal time for NPT run? My question might sound trivial but i need to know if this makes a difference. I want to simulate protein for 50ns. So, prior to final mdrun, how long NPT run is required? Sent from my iPhone > On 26-Jan-2016,

Re: [gmx-users] how to modify the code to generate more controllable checkpoints to restart?

I suppose the TRR file, which you can write down at given frequency, contains the same information with the same precision as it is written down to the CPT file. On Tue, Jan 26, 2016 at 7:50 AM, Yong Wang wrote: > Hi, > > I'd like to restart the MD simulation from some

[gmx-users] Deuterium order parameter for DPPC

Hello Everyone, I am facing a problem while calculating the order parameter in case of DPPC. I have defined the atom in the index file properly. But the problem is that i have defined atom index for 18 atoms and m getting order parameter for only 16 atoms. I am not getting what mistake i have

Re: [gmx-users] how to modify the code to generate more controllable checkpoints to restart?

Hi, There's no need to modify the code to do this. You can schedule your own halt e.g. 10ns from the end by choosing nsteps, save that checkpoint file, and then continue. That's slightly wasteful of computer time, doing extra shut-down and start-up work, but you can have it working in five

Re: [gmx-users] Gromos96 53a6 and Berger Lipids

Hi Tom, hi all, thanks a lot for your answer, it helped a lot. Regarding the issues with some of the other lipid parameters provided in the Kukol paper (POPC/POPG parameters), I would be happy if you could point me to the papers you have in mind. Best regards and have a nice day, Moritz

Re: [gmx-users] Gromos96 53a6 and Berger Lipids

Hi Moritz, For PG, issues with the Kukol parameters are briefly mentioned in the Supporting Info of: http://pubs.acs.org/doi/abs/10.1021/jp207013v some of which (in particular the dihedrals around the double bond) are discussed in more detail for POPC in:

Re: [gmx-users] Temperature or Pressure Coupling

yes On Tue, Jan 26, 2016 at 3:42 AM, sun wrote: > Hello > I want to simulate a protein in water and observe its behavior alone and > then in the presence of ligand. I have read somewhere that NPT MD is best > for pro-lig complexes as it resembles the in vitro and in vivo

[gmx-users] how to modify the code to generate more controllable checkpoints to restart?

Hi, I'd like to restart the MD simulation from some time points (e.g. 10ns before the end) but with minorly adjusted parameters. But it seems the current Gromacs code can't do this right now. I am trying to understand how the checkpoints in gromacs work. But I only found very limited document

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 115

Thank you so much Justin for your reply, I am so sorry it is DOPC not DPPC , i did a mistake while posting the querry. When i am calculating order parameter for DOPC i am getting order parameter values only for 16 atoms. But in several papers (J. Chem. Theory. Comput. 2012, 8, 2938-2948) order

Re: [gmx-users] Deuterium order parameter for DPPC

On 1/26/16 6:26 AM, Him Shweta wrote: Hello Everyone, I am facing a problem while calculating the order parameter in case of DPPC. I have defined the atom in the index file properly. But the problem is that i have defined atom index for 18 atoms and m getting order parameter for only 16

Re: [gmx-users] how to modify the code to generate more controllable checkpoints to restart?

Hi, Vitaly's suggestion is incomplete, inasmuch as there are things like thermodynamic coupling algorithms that need to preserve information across restarts that are not x/v/f, so don't get written to the .trr file. In the old days, those were written to the .edr file, and the combination of .edr

[gmx-users] refining a TI calculation - additional lambda points

Dear All, I was wondering if you have tips on how to easily create additional lambda points in a thermodynamic integration calculation in gromacs 5. I have 21 lambda points already simulated, from L_0 to L_20, and now I need six more lambda-points between L_16 and L_19. Cheers, oliwia --

Re: [gmx-users] how to modify the code to generate more controllable checkpoints to restart?

The phase space state is defined by momenta and coordinates of all objects in a dynamical system. Regarding what people call exact continuation, you are welcome to compare both solutions using small runs. I doubt that the difference in any property of interest will be observable.

Re: [gmx-users] how to modify the code to generate more controllable checkpoints to restart?

Hi Mark, It makes sense. Thanks a lot for your nice comments. cheers, Yong 2016-01-26 15:39 GMT+01:00 Mark Abraham : > Hi, > > Vitaly's suggestion is incomplete, inasmuch as there are things like > thermodynamic coupling algorithms that need to preserve information

Re: [gmx-users] refining a TI calculation - additional lambda points

On Tue, 26 Jan 2016 15:47:03 +0100 Oliwia Maria Szklarczyk wrote: > Dear All, > > I was wondering if you have tips on how to easily create additional > lambda points in a thermodynamic integration calculation in gromacs > 5. I have 21 lambda points already simulated, from L_0

Re: [gmx-users] how to modify the code to generate more controllable checkpoints to restart?

Indeed. So that includes the space itself. The unit cell (pressure coupling state) and the heat bath (thermostat state), etc. The corresponding _positions_ and _momenta_ are rather elusive, but they can be kind of captured in parameters that are transferred across a restart. Cheers, Tsjerk On

[gmx-users] cannot find AVX compiler flag

Hi, I have a server with suse enterprise linux, two zeon cpu (2630) and a gpu (gtx titan x). I tried to install gromacs 5, but the following error appeared: cannot find AVX compiler flag, how can I fix the error? best regards, -- *** sako mirzaie

[gmx-users] Question

Hello Gromacs users, When running pdb2gmx, what determines the function number used for each type of potential (bonds, angles, dihedrals, etc.). When I run pdb2gmx, my dihedrals section is built with function number 3. I would like to change this to function number 5. It is easy to edit the file

Re: [gmx-users] Question

On 1/26/16 2:51 PM, Eric Smoll wrote: Hello Gromacs users, When running pdb2gmx, what determines the function number used for each type of potential (bonds, angles, dihedrals, etc.). When I run pdb2gmx, my dihedrals section is built with function number 3. I would like to change this to

Re: [gmx-users] cannot find AVX compiler flag

You provide no details, so anyone can only guess, but it's likely that you have outdated compiler and/or binutils. Also, the question that was answered just yesterday. Please take the time to i) provide details and ii) search the list before asking. -- Szilárd On Tue, Jan 26, 2016 at 7:25 PM,

Re: [gmx-users] Placing water molecules in a defined space in the model

On 1/26/16 7:58 PM, Agnivo Gosai wrote: Hello users, I am trying to prepare a topology containing an alkanethiol layer and a protein moelcule above it for a MD simulation using GROMACS 4.6.7. For this, I want to place the water molecules in the layer in such a way that they only occupy the

[gmx-users] Using Lincs

Dear Users, I am using gromacs to simulate Ionic liquid, [BMIM][PF6], inside confinement using OPLSA-AA forcefield, I want to know whether using Lincs for bonds is correct or not. Best Regards, Alireza Moradzadeh -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Blender Molecular Visualization Workshop at VizBi 2016

Hi all! Just want to let you know that Chris Hammang (check out his animations!) and me are giving a Blender Workshop at VizBi 2016 - 9th March - in Heidelberg where we will also cover molecular visualization. The special aspect about this workshop is: it is divided into two parts: 1) for

Re: [gmx-users] MDRUN warning during minimization

Hi, I checked the link provided by Dr. Justin. The below mentioned lines are from the help in that link: "There can be a number of reasons for the large velocities in your system. If it happens at the beginning of the simulation, your system might be not equilibrated well enough (e.g. it

Re: [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3

Hi, After installing the last version of binutils, it worked. Thanks for the tip. Nicolas PS: Just in case, to be able to install binutils I had to follow the instructions given here

Re: [gmx-users] how to modify the code to generate more controllable checkpoints to restart?

Hi Mark, thank you very much. It is really a good way to do it without touching the code. Although as you said, it is not a perfect solution, but I think it is sufficient to do what I want. Also thank you Vitaly for your comment. But I am not quite clear about the difference between the .cpt file