Re: [gmx-users] Atom positions change between topology generation and NVT equilibration

Hi Max, In the .mdp file that you uploaded you are using constraints = h-bonds   ; bonds involving H are constrained Is that the right file? Otherwise running without these constraints might help. On the off-chance that happened: not using -ignh in grompp avoids re-placement of

Re: [gmx-users] debugging

Hi Miro, This can be of great help and a wonderful learning experience; at the same time also an enormous time-sink. First, you did already do a bunch of very helpful work in trying to find the latest version, where things still work,  have the error be reproducible on a test system. If y

Re: [gmx-users] lincs warning

Hi Afsane, This might be an issue with the pressure coupling, depending on the compressibility you give for your system and the algorithm that you use for pressure coupling you might see quite large fluctuations in pressure. One idea might be to use temperature coupling to quickly dissipate

Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1

Hi Yujie, This sounds very much like something we should fix. Can you file a bug report at https://redmine.gromacs.org/ where you can also upload the file that you are trying to run? Let me know if you have any trouble with uploading the report - I'm eager to know what happened. Best, Chr

Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1

Hello Yujie Liu, I am guessing the issue a bit from the brief title, let me know if installing the external program required to run dssp as described below is addressing the issue or if this is something that used to work in GROMACS 2019 and suddenly stopped working, in which case I would nee

Re: [gmx-users] mdp option periodic molecules

Hi Johannnes, That is correct. Another confirmation of what you already suspect is found in the manual in http://manual.gromacs.org/documentation/current/reference-manual/topologies/molecule-definition.html

Re: [gmx-users] Listing residues in gromacs

Hi Subhomoi, Yes, gmx select can do that (see http://manual.gromacs.org/documentation/2020/onlinehelp/gmx-select.html) For what you want to do, it's beneficial to have a look at the selection syntax here http://man

Re: [gmx-users] Keeping more than 1 version of gromacs on single os UBUNTU

Hi Navneet, This is achieved by setting the installation directory with cmake for the respective source code that you downloaded, then sourcing different GMXRC. Install different GROMACS builds fromt the source code into seperate folders using something like -DCMAKE_INSTALL_PREFIX=/home/navne

Re: [gmx-users] (no subject)

Hi Shakkira, The simulation box deformation is described by six parameters that describe three basis box vectors with the following contraints,  - the first box vector is aligned along the x-axis, with coordinates thus has coordinates (xx,0,0)  - the second box vector is aligned in the x-y

Re: [gmx-users] genion without stdin

Hello Matthias, yes, if you use an indexfile with exactly one index group inside, this index group will be automatically picked. (like [ solvent ] 1001 1002 1003 1004 1005 1006 1007 1008 1009  ... and nothing else Best, Christian On 2020-02-13 11:49, Urban, Matthias wrote: Hello mail

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 189, Issue 80, 2. Re: Analysis with .sh file (Li, Shi)

HI Riccardo, in this case, it's the piping that does not work, so gromacs does not get the right "return". An alternative is printf "10\n12\n" Best, Christian On 2020-01-31 09:22, ric.co...@gmail.com wrote: Dear all, This is an example of a line I have been using on Gromacs 5.0.4:" echo

Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

Hi Michele, Thanks for the input and suggestion! I created a redmine issue using your observations that you can follow at https://redmine.gromacs.org/issues/3353 Best, Christian On 2020-01-23 11:03, Michele Pellegrino wrote: Ok, I believe I have found the nature of this 'quirk' looking

Re: [gmx-users] specific heat calculation using "gmx dos"

Hi Pragati, Answers in short: 1. It's only c_v, you'll have to add VT \alpha_T^2/ \kappa_T to obtain c_p 2. I suggest you use the approach in the paper, running an NVT simulation and base all on the c_v estimate. 3. To check convergence, I suggest running the analysis again on shorter parts

Re: [gmx-users] State of Matter

Hi Sina, You can have a look at order parameters of your system like angular distributions, orientations, local densities, etc. with analysis tools like gmx angle, h2order, order. Best, Christian On 2020-01-20 12:02, Sina Omrani wrote: Hi, I'm new to GROMACS and Molecular Dynamics and I'm

Re: [gmx-users] gmx genconf

Hi Alex, It's not possible with genconf. genconf only ever outputs a single structure. If you provide a trajectory, each frame in the trajectory is matched with a grid position that is then output as a single structure. If you're looking into this for the sake of visualisation, tools like v

Re: [gmx-users] Visualize replica exchange

Hi Ahmed, I don't know about VMD, but you can try ./gromacs/scripts/demux.pl Best, Christian On 2020-01-09 15:01, hind ahmed wrote: Dear All, How can I visualize replica exchange in VMD? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] Replica exchange probabilities and extend simulation

Hi Ahmed, If you have a look into "Optimal temperature ladders in replica exchange simulations", available here: https://www.sciencedirect.com/science/article/pii/S000926140900356X you will see that your exchange probabilities should be a bit higher. Then again, you might have to set up a lot

Re: [gmx-users] cant compute msd

Hi Devargya, I believe it's the mixture of -mol and -o options at the same time that leads to the unexpected behaviour - there can only be one .xvg output for this tool and we'll see to having it fixed. Do you get any diff_mol.xvg files instead? The documentation states that "If -mol is se

Re: [gmx-users] How to rotate the molecule in box

Hi Yeping, The center of rotation is (0,0,0) for the rotate command, which is the lower left front corner of your box, and not the box center. That's why the molecule moves out of the box when rotating. One (of conceivable more ways) to perform the rotation, is to use -center (0,0,0) to creat

Re: [gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

Hi Navnett, gmx select will be your friend. At the bottom of http://manual.gromacs.org/documentation/current/onlinehelp/selections.html you'll find some example commands. Something along the lines of   gmx select -select 'name CA and resid > 149 and resid < 211' should work. It's a very

Re: [gmx-users] Make index command in gromacs

Hi Shan, gmx select gives you many more options to do complex arithmetic with selections that might help you here. You can try using gmx select -select "SELECTION STING" you'll find lots of selection string examples at the bottom in here: http://manual.gromacs.org/documentation/current/onl

Re: [gmx-users] Trajectory guided by density maps

ransition. I mean, I figured I would need to gradually switch on one map while switching off the other, but for this I need to apply both restraints at the same time right? Do you see another way of doing this? Best, Ramon On Thu, Dec 12, 2019 at 12:23 PM Christian Blau wrote: Hi Ramon, This feat

Re: [gmx-users] Trajectory guided by density maps

ample or a default set of values for the density-guided options? I am not really sure how to use this feature anyway... Thanks! R On Thu, Dec 12, 2019 at 11:29 AM Christian Blau wrote: Hi Ramon, This is definitely a way to obtain a transition path. One things to consider here is that you

Re: [gmx-users] Trajectory guided by density maps

Hi Ramon, This is definitely a way to obtain a transition path. One things to consider here is that you deliberately "throw away" already perfect information about your target structure, so it might be harder to reach. On the other hand you might not care to have an exact overlap with the str

Re: [gmx-users] Chemical Shifts prediction using gmx chi -shift

Hello Florent, The tool is based on  "D. S. Wishart and A. M. Nip", "Protein Chemical Shift Analysis: A Practical Guide", "Biochem. Cell Biol.", 76, 1998, "153-163" It reads chemical shift reference data on a phi-psi-angle grid from ca-shift.dat, cb-shift.dat, ha-shift.dat and co-shift.dat.

Re: [gmx-users] Help installing do_x3dna

Hi Salvador, If you did not have any luck so far, trying to contact the author of the tool, Rajendra Kumar, directly might help: https://scholar.google.com/citations?user=zYKuBCcJ&hl=en Best, Christian On 2019-11-21 21:00, Salvador Herrera-Velarde wrote: Dear All, I am trying to insta

Re: [gmx-users] How to calculate the spatial distribution function for the last 50ns of the trajectory?

Hi Peiyin, There is a related redmine entry that suggests this might be fixed in newer versions of GROMACS https://redmine.gromacs.org/issues/2189 (from GROMACS2018 on). If you are using a newer GROMACS version, to rule out that this is an issue related to .tng, can you try using the older .

Re: [gmx-users] Maximising Hardware Performance on Local node: Optimal settings

Hi Matt, Here are a few bullet points that might help you, maybe other experts can contribute more. If you're running on a single machine, using thread-mpi over mpi is a good choice. "-pin on" might help you. 60k atoms is not very large, here are some other systems ready to benchmark https

Re: [gmx-users] npt.tpr protein-lig

Hi Iman, Great that you checked the notes! The oscillatory period is estimated only from the masses and the force constant for the bond, see https://socratic.org/questions/frequency-of-vibration-of-two-masses-connected-by-a-spring ; note that the oscillation period = 2pi/\omega. To be on the

Re: [gmx-users] Problem with GROMAC 2019.4

HI Avneel, In general, using the latest stable version is always the first thing to recommend, because this is where your issue might have already been fixed. Do you also get the same "unsafe srcdir value" when running make? It'd be interesting to know what system you are using. I assume

Re: [gmx-users] the a.u. unit in the RMS distribution graph

Hello Lalehan and Justin, Thanks for the suggestion! The following patch : https://gerrit.gromacs.org/c/gromacs/+/14542 does exactly that. Best, Christian On 2019-11-29 14:23, Justin Lemkul wrote: On 11/29/19 7:18 AM, Christian Blau wrote: Hello Lalehan, a.u. stands for "arbi

Re: [gmx-users] the a.u. unit in the RMS distribution graph

Hello Lalehan, a.u. stands for "arbitrary units". The rmsd-dist contains a histogram over the distribution of rmsd values, you can read the a.u. as counts per length-interval. Best, Christian On 2019-11-29 12:57, Lalehan Ozalp wrote: Hello everyone, I ran a cluster analysis for a 10 ns s

Re: [gmx-users] Magnetic effects in a classical force field

Dear Yogesh, This question strays indeed a bit from the forum topic though being valid. In short - the effect is too small to be considered. The interaction terms in a force field are usually developed as approximations to the the non-relativistic coulomb molecular Hamiltonian operator. In t

Re: [gmx-users] Superparamagnetism

Dear Amin, Superparamagnetism can not be simulated easily with GROMACS. Some challenges you'll face are the following:  - Usual superparamagnetic materials like iron oxide nanoparticles require a quantum chemistry parametrization that will be hard to approximate with classical force field  

Re: [gmx-users] droplet

Hi Alex, I'm not sure this is really something for the GROMACS mailing list and I'm guessing the question you were asking - What is the expected behaviour of the solvent accessible surface area of a droplet with temperature? Here is a "back-of-the envelope" estimate: The easiest model of a dr

Re: [gmx-users] eelctric field

applied the filed in x direction and I have NVT ensemble). So I think the way Gromacs calculates the pressure in presence applied field does not take into account the field effect, am I correct? On Fri, Nov 15, 2019 at 11:17 AM Christian Blau wrote: Hello Amin, Though the forces are present

Re: [gmx-users] Regarding LSI calculation

Hi Omar, Though I don't know of any GROMACS tool that can calculate the local structure index, some third-party tool might help, like https://pypi.org/project/iOrder/ The input file format for above tool is .xyz which you can obtain from a GROMACS trajectory using the MDAnalysis tools here:

Re: [gmx-users] Potential bug in IMD implementation (Interactive Molecular Dynamics)

Hi Xavier, Bugs are usually best reported via "redmine.gromacs.org". You can self-report when registering there. In this case I just went ahead and filed the bug report, if you want to add information to the bug report and check how things are developing you can check here: https://redmine.g

Re: [gmx-users] applied electirc field with use potential

Hi Amin, It's me again :) Yes, applying an electric field mixes well with any other potentials you apply. When you use an additional electric field by using the .mdp options, there is already an additional force added to all the forces on the atoms that makes the system respond to an electric

Re: [gmx-users] eelctric field

similar values of energies (LJ, columbs, total energies) while a different pressure, with and without applied filed? The total energy should be different as a result of an additional energy due to applied filed on each atom. On Wed, Nov 13, 2019 at 3:10 PM Christian Blau wrote: Hello Amin, When you

Re: [gmx-users] eelctric field

Hello Amin, When you apply an electric field during the simulation by setting the mdp parameters like E-x =... as you describe, nothing more happens than that each atom experiences an additional force that is "atom charge * field strength". The energy terms or virial (that then would relate to

Re: [gmx-users] Script to merge protein and ligand topology for BAR calculation?

Hi Billy, I cannot offer a script for the merging of the topologies, but depending on the transformation you want to carry out, I can suggest using pmx http://pmx.mpibpc.mpg.de/webserver.html for preparing dual topologies for alchemical free energy calculations that are GROMACS-compatible.

Re: [gmx-users] (no subject)

Hello Shakuntala, If you already have the trajectories, you have to post-process at least once to filter the data down to a manageable size, and once to do the periodic boundary condition fix precisely as you described. If you set up a new simulation you may use "nstxout-compressed" to contro

Re: [gmx-users] gmx trjorder

Hello Akash, Not knowing much more about your this system, this looks reasonable to me and should give you the count you just described. Best, Christian On 11/7/19 2:44 PM, Pandya, Akash wrote: Hi, I would like to calculate the number of ligand molecules within 0.5 nm of a particular ami

Re: [gmx-users] Stochastic Dynamics nsttcouple

Hi John, Thanks for the suggestion! Find a patch here that updates the mdp documentation to clarify the issue you had with nsttcoupl: https://gerrit.gromacs.org/c/gromacs/+/14157 Let me know if things are still unclear. Best, Christian On 11/7/19 1:38 PM, John Whittaker wrote: Hi Justin

Re: [gmx-users] Load Imbalance

Hello Shradheya, If you want to enforce dynamic load balancing you can use gmx mdrun -dlb yes instead of the default "auto". However, as I read from the output, your system was not balanced because it was not needed and the overhead of re-distributing atoms might outperform the gain from it.

Re: [gmx-users] Time step mismatch.

Hello Maryam, trjconv might help here. There are two ways I can interpret time step in your email.  1. the integration time step dt - if you changed this one I would not recommend that you concatenate the trajectories (though also possible), but treat this as independent simulation setup, bec

Re: [gmx-users] gmx gangle in a for loop

Hello Alex, What works for me is setting '$i' within singe quotation marks, e.g., 'group '$i' and name C10 plus group '$i' and name C20' Note that this is more of a bash escaping quotes issue and only a GROMACS issue insofar as the selection syntax requires the quotes. Best, Christian O

Re: [gmx-users] Output from gmx h2order

Hello Decai, h2order works in the following way:   - all water molecules are put into the simulation box by applying periodic boundary conditions so that the first water molecule atom is in the simulation box   - the simulation system is sliced along z (0,0,1) direction (default, can be cha

Re: [gmx-users] Simulated Annealing General Procedure

Hello Neena, The outline you give appears reasonable for exploring peptide conformations. It is very hard to judge appropriateness though without knowing what you are trying to learn from your system. The unspecified position restraints might defeat the purpose of the simulated annealing if y

Re: [gmx-users] (no subject)

Hello Saranya, Now again with readable formatting. Also note that it is very useful to people on gmx-useres to specify the subject when writing emails, because it makes it easier to search, reply, and handle multiple discussion threads. This error means that during the nvt equilibrium high fo

Re: [gmx-users] how to perform analysis in faster with multicore/processor

Hello Nikhil, Currently there is no "in-built" way to do this. (we thought of this before and there is some basic infrastructure for this in the trajectory analysis framework, but in short - no) However, if you have many trajectories you can run analysis of all trajectories in parallel to spe