Re: [gmx-users] -t option?

Hi Hadi, to expand a little on Mahdi's (correct) answer: The checkpoint file contains coordinates and velocities in full precision (unlike .gro and .xtc files). In addition, it contains the state of the thermostat and barostat (if applicable). The thermo/barostat states are not present in the

Re: [gmx-users] Issues with energy minimization of a membrane protein

"Maximum force =inf on atom 3999" is the hint Gromacs gave you. This means that atom 3999 (and possibly more) have very bad overlaps. This is backed up by your LJ energy being very high. Use VMD (or something similar) to inspect that atom and it's surrounding. Peter On 16-09-19

Re: [gmx-users] Coarse-grained Protein-ligand simulations

, and you will need to >>> do >>>>> extensive validation on the topologies of your ligands. Again, it >>> depends >>>>> on your exact research question: if you’re doing high-throughput like >>>>> screening, qualitative models might be

Re: [gmx-users] Coarse-grained Protein-ligand simulations

Lemkul, > > I appreciate your comment on this part. > > Sir Peter Kroon, > > We want to do the coarse-grained MD simulation to access long timescale > events of the > effect of the ligand binding to the GPCR, at least microsecond . For now, > the most accessible means for us i

Re: [gmx-users] Coarse-grained Protein-ligand simulations

If I may chip in: It really depends on what you're studying, and what forcefield you're using to do it. Unfortunately there is no FF that reproduces all behaviour accurately. The art is in picking one that (at least) reproduces what you're interested in. Peter On 29-03-19 17:26, Justin Lemkul

Re: [gmx-users] CG lipid diffusion coefficient

Dear Yasser, A factor of 100 is kind of a lot indeed, and should prompt further investigation. What phase (gel, liquid disordered, ...) is your bilayer in? Is it homogeneous? Is it the same as the phase for your reference value? The 2009 paper probably uses a different mapping scheme/topology

Re: [gmx-users] Bond breakage modelling

est regards, > Ali > > > >> On 19 Feb 2019, at 11:35, Peter Kroon wrote: >> >> Hi Ali, >> >> >> The short answer is "not really". You could model your bonds as >> non-bonded (morse) potentials, but then you lose all angle depend

Re: [gmx-users] Bond breakage modelling

Hi Ali, The short answer is "not really". You could model your bonds as non-bonded (morse) potentials, but then you lose all angle dependence on the potential energy, since the non-bonded potentials must be pair-wise. Depending on the exact problem this may be acceptable though. The angle

Re: [gmx-users] Do hydrogen bonds innately exist using mdrun?

Hi James, hydrogen bonds are an intrinsically quantum phenomenon, and are more like a partial covalent bond than anything else. (According to NMR experiments. Polarisation is transfered across H-bonds). The good news is that for most purposes MD water "just works". Even though the exact

Re: [gmx-users] gmx trjconv -center not working?

What does "gmx energy -b 2 -e 2" give as box dimensions? Peter On 07-02-19 22:20, Mala L Radhakrishnan wrote: > Hi Justin, > > Thank you -- the good news is that the center of mass of this group does in > fact match what I calculate to be the COM with my script. > > BUT, the bad news is

Re: [gmx-users] Position restrained energy minimization

That will still allow peptide atoms to move (if only a little). AFAIK Gromacs is not really fit for rigid body studies, but you can set all bonds and angles to constraints (mdp option: constraints=all-angles). This may or may not work. Torsion angles will still be free to rotate though. From the

Re: [gmx-users] martini: what is the column position if "ASP" is changed to "ASP0" in the itp file?

Hi Cheng, ITP columns are whitespace separated. So it doesn't matter which character column it is in exactly, so long as it's separated with whitespace from the other elements. See http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#topology-file Peter On

Re: [gmx-users] How to adjust the default protonation states in martini itp files?

I got an answer :) > The GLU0 is good indeed. For the termini, it depends on the secondary structure. Coil is the most likely for a terminus, so P5 should be OK. Note that there is a -nt option in martinize that sets neutral termini. > Jonathan Peter On 29-01-19 10:44, Peter Kroon wrote

Re: [gmx-users] How to adjust the default protonation states in martini itp files?

Hi Zhang, I'm fairly sure GLU0 does what you want, but I'm not 100% sure on the terminus. It'll probably do what you want, but I've forwarded your question to the group to be sure. Peter On 29-01-19 01:38, ZHANG Cheng wrote: > Dear martini friends, > > > By default, the "martinize.py" will >

Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

Hi all, @Fotis, the softcore potential for minimization sounds interesting, I'll remember that! Alternatively, something we also occasionally do in the lab, is replace all constraints for stiff bonds during minimization and if needed the first bit of equilibration. Peter On 22-01-19 13:24,

Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

Hi, You can reduce the timestep during equilibrations to e.g. 10 fs, or 5 when you have a really bad starting configuration. Bring it back up to 20 (in steps if needed) before starting your actual equilibration/production though. In addition, you can raise the lincs_order to 8. And yes, the

Re: [gmx-users] contact analysis between the all backbone of same protein

anges. > thanking you > shahee > > On 12/19/18, Peter Kroon wrote: >> Hi Shahee, >> >> >> what cutoff do you mean? >> >> You can find sample Martini MDP files here: >> http://cgmartini.nl/index.php/force-field-parameters/input-parameters. >> >

Re: [gmx-users] contact analysis between the all backbone of same protein

Hi Shahee, what cutoff do you mean? You can find sample Martini MDP files here: http://cgmartini.nl/index.php/force-field-parameters/input-parameters. The normal VDW and coulomb cutoffs are 1.1 nm. Peter On 19-12-18 09:30, SHAHEE ISLAM wrote: > thank you so much for your reply. > I have

Re: [gmx-users] Running Grompp in reverse and backing up MD data

at 3:16 PM Justin Lemkul wrote: > >> >> On 11/29/18 6:43 AM, Peter Kroon wrote: >>> Hi Mark, >>> >>> thanks for the rapid reply! >>> >>> Hmmn. It doesn't have to be exactly matching input. An equivalent to >>> e.g. mdout.mdp prod

Re: [gmx-users] Running Grompp in reverse and backing up MD data

> > On Thu, Nov 29, 2018 at 11:27 AM Peter Kroon wrote: > >> Hi all, >> >> >> In the lab we're thinking about backup solutions for MD data (and in >> particular gromacs produced data). Since trajectories tend to be large >> we quickly decided that backi

[gmx-users] Running Grompp in reverse and backing up MD data

Hi all, In the lab we're thinking about backup solutions for MD data (and in particular gromacs produced data). Since trajectories tend to be large we quickly decided that backing up the results of simulations is a waste of disk space. Instead, we'll probably go for backing up the TPR files.

Re: [gmx-users] secondary structure analysis

No, this is not correct. Prehaps I worded my first e-mail too subtly. The secondary structure of a protein in a normal Martini simulation *will not* change. Trying all sorts of tricks to make the analysis program happy will not change this. The secondary structure is fixed by your topology.

Re: [gmx-users] Problem while equilibrating system with frozen groups

Hey Arnab, Why do you freeze atoms instead of putting position restraints? Why not let the loose entirely? Freezing creates large artefacts. Second, 4 ns equilibration is *way* too short. Lastly, see http://www.gromacs.org/Documentation/Terminology/Pressure Peter On 10-09-18 19:01, ARNAB

Re: [gmx-users] GMXRC removes trailing colon from existing MANPATH

Hi, > > Can you please submit your change to gerrit.gromacs.org -- and perhaps it's > best if you also file an issue on redmine.gromacs.org with your brief > description you posted here? > > Thanks, > -- > Szilárd > > > On Fri, Jul 27, 2018 at 2:28 PM Peter Kroon

[gmx-users] GMXRC removes trailing colon from existing MANPATH

Hi all, I noticed that sourcing GMXRC removes any trailing colons from a set MANPATH environment variable. This colon *is* syntactically significant, and removing it causes `mandb` to ignore /etc/manpath.config instead of appending that file: > unset MANPATH > export

Re: [gmx-users] REPOST Coarse graining carbon nanotubes and MARTINI

Hi Raman, I forwarded your question to some people off list, and chance has it I just got a reply back! So with a big thanks to R. Alessandri and M. Vögele! Peter Hi, 1.)  We made a tool to create Martini models for open carbon nanotubes:  https://github.com/bio-phys/cnt-martini. The

Re: [gmx-users] GMX 2018 regression tests: cufftPlanMany R2C plan failure (error code 5)

> > It will really suck, if these are hardware-related... > > Thanks, > > Alex > > > On 2/8/2018 3:03 AM, Mark Abraham wrote: >> Hi, >> >> Or leftovers of the drivers that are now mismatching. That has caused >> timeouts for us. >> >> Mar

Re: [gmx-users] Problem with Gromacs and Charmm force field dump rates

Hi Vivien, My answers are inline On 08-02-18 12:28, Vivien WALTER wrote: > Dear all, > > We are experiencing a strange problem with all-atom simulations using > Gromacs and Charmm force field, and we have trouble to sort it out. > > We are simulating a single-ring sugar and we observe

Re: [gmx-users] GMX 2018 regression tests: cufftPlanMany R2C plan failure (error code 5)

Hi, with changing failures like this I would start to suspect the hardware as well. Mark's suggestion of looking at simpler test programs than GMX is a good one :) Peter On 08-02-18 09:10, Mark Abraham wrote: > Hi, > > That suggests that your new CUDA installation is differently incomplete.

Re: [gmx-users] paralllelized gromacs run creating same file in many times -reg

e. Additionally, setting cmake > -DGMX_MPI=on will make sure that you can't accidentally build a non-MPI > version of GROMACS. > > Mark > > On Thu, Feb 1, 2018 at 11:40 AM Peter Kroon <p.c.kr...@rug.nl> wrote: > >> Hi Venkat, >> >> >> I've s

Re: [gmx-users] paralllelized gromacs run creating same file in many times -reg

Hi Venkat, I've seen similar behaviour with OpenMPI and a home-patched version of Gromacs. I blamed OpenMPI/the cluster and contacted the admins (but I don't remember what the result was). In the end I solved/worked around the issue by compiling Gromacs with IntelMPI. HTH Peter On 01-02-18

Re: [gmx-users] Measuring distance to the nearest image

Hi Anthony, I assume you've seen the -pbc flag of gmx distance; and IIRC there's also some options for that in the selection syntax. I'm not sure that'll do what you want though. If you're going to make a script, have a look at the Python module MDAnalysis, that has some nifty tools. If you

Re: [gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?

On 24-11-17 13:48, Justin Lemkul wrote: > > > On 11/24/17 5:25 AM, ZHANG Cheng wrote: >> Dear Justin, >> Thank you for confirming this. May I ask, >> >> >> 1) How to "fit to the whole protein (or backbone, CA, etc) and >> subsequently calculate the RMSD of given residue(s)"? >> >> >> My current

Re: [gmx-users] Handling Periodic Boundary Conditions

Hi Akash, a cheap trick you can try (depending on your system) is to center your trajectory on some residue or atom in the middle of your protein/assembly/... Otherwise it sometimes helps to invoke trjconv multiple times. First with e.g. -pbc whole, and a second time with -center. Peter On

Re: [gmx-users] Inconsistency in units of virtual sites?

Hoi Douwe, according to the manual the units are indeed inconsistent (but documented, and therefore ok). See table 5.5 of the manual. For 3out the unit of c is in nm^-1. Peter On 21-11-17 10:15, Douwe Pollmann wrote: > Thanks Justin for the reply. > > I'm sorry for the inconvenience, I put

Re: [gmx-users] convergence of PMF

On 17-11-17 14:48, Justin Lemkul wrote: > > > On 11/17/17 8:47 AM, Peter Kroon wrote: >> >> On 17-11-17 14:38, Justin Lemkul wrote: >>> >>> On 11/17/17 6:28 AM, abhisek Mondal wrote: >>>> Hello, >>>> >>>> I understand th

Re: [gmx-users] convergence of PMF

On 17-11-17 14:38, Justin Lemkul wrote: > > > On 11/17/17 6:28 AM, abhisek Mondal wrote: >> Hello, >> >> I understand the invariant trend is the key feature to look out for >> in this >> case. >> >> But, is it possible to comment on the convergence from Force-vs-Time >> plot ? >> I mean, if I

Re: [gmx-users] convergence of PMF

Hi, you can check whether the forces of the windows (pullf.xvg files) have converged. Peter On 16-11-17 09:34, abhisek Mondal wrote: > Hi, > > I have derived a PMF (protein-ligand) using umbrella sampling method. > But how can I comment if the obtained PMF has converged well ? What are

Re: [gmx-users] only interaction inside the molecule

Hi Faezeh, have a look at the [pairs] or [pairs_nb] directives. Table 5.5 in the manual. Note that these directives will be in your molecule itp (in the [moleculetype] section). Peter On 09-11-17 10:30, Faezeh Pousaneh wrote: > no that is not my answer Yu. > > for example I would like to

Re: [gmx-users] Writing pdb snapshot with charge from gro trajectory

IIRC the pdb format only allows 1 character (2 with sign) for the charge, so you can only use integer charges. Which is pretty useless in a MD context. So note that if you write a "pdb" with partial charges, you're not writing pdb anymore, and I doubt anything other than handcrafted programs will

Re: [gmx-users] gmx trjconv to produce tng produces segfault

Thanks Mark. I added my files and description to https://redmine.gromacs.org/issues/2187. Peter On 12-10-17 12:02, Mark Abraham wrote: > Hi, > > On Thu, Oct 12, 2017 at 11:26 AM Peter Kroon <p.c.kr...@rug.nl> wrote: > >> Hi all, >> >> I'm trying to produc

[gmx-users] gmx trjconv to produce tng produces segfault

Hi all, I'm trying to produce a tng file from my trajectory (can mdrun write those directly yet?) since VMD likes those better for coarse grained systems. I'm not interested in my solvent, so I select a smaller group for my output. When I run the following commands it produces a segfault. If I

Re: [gmx-users] How to recover a corrupted .edr file

Hi Christopher, can you regenerate the edr file using -rerun and your salvaged trajectory? That might be the easiest solution. Peter On 05-10-17 07:38, Christopher Neale wrote: > Dear users: > > > I recently experienced some corruption in a .xtc and a .edr file. Recovering > the .xtc was

Re: [gmx-users] continue simulation from intermediate frame instead of last frame

Hi MY, actually you lose continuity of your simulation in both cases. The cpt file stores full precision coordinates and velocities (unlike gro/xtc). In addition, it stores state information about the simulation itself, such as the themostat and barostat. Whether this is an issue is up to you of

Re: [gmx-users] Topology and co-ordinates do not match

rce > field that will have one) > 2. A [system] directive > 3. A [molecules] directive > > This is the primary difference between the two. > > -Justin > >> Natalie >> >> On 20 September 2017 at 12:54, Peter Kroon <p.c.kr...@rug.nl> wrote: >> &g

Re: [gmx-users] Topology and co-ordinates do not match

of 47 atoms at the end of the gro file. The ligand is carried through into > the subsequent co-ordinate files, but as soon as I hit grompp I have an > issue. > > Natalie > > On 20 September 2017 at 12:42, Peter Kroon <p.c.kr...@rug.nl> wrote: > >> Hi Natalie, >> &g

Re: [gmx-users] Topology and co-ordinates do not match

Hi Natalie, did you change the particle count on the second line of your gro file? Peter On 20-09-17 13:31, Natalie Tatum wrote: > Dear all, > > I have what appears to be a common problem but I can't seem to track down > the solution. The number of coordinates in my coordinate file >

Re: [gmx-users] Gromacs_GPU_Compiling_Problem

Hi, you (tried to) compile gromacs 5.1.4; but your mdrun says it's version 5.1.2. Somewhere something is wrong. Did you source your new GMXRC from the version you compiled and installed? Peter On 22-08-17 10:36, Nikhil Maroli wrote: > Hi, > Your log file did not show any GPU card. which

Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

> manually through combining the building blocks available within the GROMOS > force field. > > Cheers > > Tom > > ________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Peter K

Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

Hi Emeliano, since you're just going to use the atomistic simulation to get some parameters for your CG model, I don't think the differences will be significant --- the approximations your are going to make in CG will be larger anyway. I would even argue you'll be better off if you run just one

Re: [gmx-users] CG to AA backmapping: problem in using initram.sh script

;30 CH2 C1 >31 CH2 C2 >32 CH2 C2 >33 CH2 C2 >34 CH2 C2 >35 CH2 C3 >36 CH2 C3 >37 CH2 C3 >38 CH3 C3 > > > Thanks for your kind and prompt reply! > > Best regards, > Sudip > > > >

Re: [gmx-users] CG to AA backmapping: problem in using initram.sh script

Hi Sudip, what's the path and content of your DET mapping file? Peter On 17-07-17 11:41, Sudip Das wrote: > Dear All, > > I forgot to mention one point in my previous mail. > > With the system containing only one detergent molecules gives me the > following error, without generating any

Re: [gmx-users] Fwd: PCA two ensembles different atoms order

ects the > PCA result. > > I don't know if it is clearer? > > Nawel > > 2017-07-03 10:44 GMT+01:00 Peter Kroon <p.c.kr...@rug.nl>: > >> Hi Nawel, >> >> >> I'm not quite sure what you're trying to achieve, or how, or what >> exactly is "wr

Re: [gmx-users] PCA two ensembles different atoms order

Hi Nawel, I'm not quite sure what you're trying to achieve, or how, or what exactly is "wrong". In general though: calculate the principle components only once, for one of the ensembles, and project both ensembles on those PCs to get comparable results. Peter On 03-07-17 11:37, Nawel Mele

Re: [gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

, then continue with 10 fs, 15fs and finally 20 fs. If that doesn't work, could you give a more detailed description of your system? Peter On 29-06-17 10:07, Peter Kroon wrote: > Hi Sudip, > > > there's a dedicated forum for these Martini questions on cgmartini.nl. > Recently there was a s

Re: [gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

Hi Sudip, there's a dedicated forum for these Martini questions on cgmartini.nl. Recently there was a similar question there (http://cgmartini.nl/index.php/component/kunena/7-mdp-options/5491-gpu-verlet-oscillational-period#7308). To summarize, the bonds between the backbone beads are extremely

Re: [gmx-users] Simulation ended prematurely, no performance report will be written- Minimization

That means your system is minimized. Or at least as minimized as it's going to get starting from this structure. Peter On 27-06-17 16:02, Alex Mathew wrote: > Dear all, > > I'm trying to minimise the CGMD system and end up with an error Steepest > Descents converged to machine precision in XX

Re: [gmx-users] CGMD with cut-off Verlet? production run stage

Hi, read the paper I sent earlier if you want to be sure. There's also a version that uses RF or PME, but they're (a bit) slower. See http://cgmartini.nl/index.php/force-field-parameters/input-parameters for the full list. Peter On 27-06-17 12:57, Mark Abraham wrote: > Hi, > > You should

Re: [gmx-users] CG MD

Backwards is one such tool http://pubs.acs.org/doi/abs/10.1021/ct400617g http://cgmartini.nl/index.php/tools2/resolution-transformation Peter On 26-06-17 18:01, Alex Mathew wrote: >> though most atomistic properties can be studied by rebuilding the > atomistic coordinates from the CG.

Re: [gmx-users] CGMD with cut-off Verlet?

For posterity, you can find a sample mdp file here http://cgmartini.nl/images/parameters/exampleMDP/martini_v2.x_new.mdp and the corresponding paper here http://dx.doi.org/10.1016/j.cpc.2015.09.014 Peter On 23-06-17 19:15, Mark Abraham wrote: > Hi, > > And follow the advice of the Martini

Re: [gmx-users] Regarding centering the molecule/protein during Simulation

n Mon, May 29, 2017 at 4:10 PM, Peter Kroon <p.c.kr...@rug.nl > <mailto:p.c.kr...@rug.nl>> wrote: > > Keep discussions on the list. > > As i wrote in my previous mail, you need `gmx trjconv -pbc mol -center > ...`. In your example this would be: > >

Re: [gmx-users] Regarding centering the molecule/protein during Simulation

Keep discussions on the list. As i wrote in my previous mail, you need `gmx trjconv -pbc mol -center ...`. In your example this would be: > gmx tjrconv -f md.xtc -s md.tpr -pbc mol -o mdx.xtc *-center* > vmd mdx.xtc If you can't figure it out from here, try `gmx trjconv -h` and read. Peter

Re: [gmx-users] Regarding centering the molecule/protein during Simulation

Hi, I would not do this. I would run my simulation as normal (no position restraints), and center my amino acid in post processing (gmx trjconv -pbc mol -center ...). You may need to make an appropriate index file. Alternatively you may want to use -fit instead of -center, but that's a matter of

Re: [gmx-users] Martini Website is not accessible

Hi, we are aware of it and will probably fix it later today. It's an update gone wrong. Peter On 22-05-17 11:44, Anurag Dobhal wrote: > Hello Gromacs users, > > This query is not related to typical gromacs error. I am unable to access > the Martini Forcefield website (http://cgmartini.nl/)

Re: [gmx-users] How to install g_fg2cg

Hi Sudip, as far as I know, fg2cg is extremely old and no longer maintained. I would suggest you look at other tools. In particular, Backwards [1] and pyCGtool [2] spring to mind. Peter [1] http://cgmartini.nl/index.php/tools2/resolution-transformation [2]

Re: [gmx-users] Fast energy evaluation

Hi, In addition to Erik's tip: once you have a tpr (made once with grompp), change it for every iteration by writing your new parameters directly to the tpr file, bypassing grompp entirely. This will require a custom script and might not be completely trivial though. Peter On 06-04-17 13:15,

Re: [gmx-users] performance issue with many short MD runs

Hi, On the new machine your CUDA runtime and driver versions are lower than on the old machine. Maybe that could explain it? (is the GPU even used with -rerun?) You would need to recompile gromacs. Peter On 27-03-17 15:51, Michael Brunsteiner wrote: > Hi,I have to run a lot (many thousands)

Re: [gmx-users] Lipid water simulation

Hi, On 27-03-17 03:55, Sheikh Imamul Hossain wrote: > Hi all, > > I am trying to simulate 1024 dppc lipids with water. I have prepared my > system using Charmm-Gui monolayer builder. Then I converted the atomistic > system to coarse grained system using bacdward.py. The box size I got in > the

Re: [gmx-users] g_energy for comparing total energies of 2 similar systems

AFAIK the total energy is usually meaningless. If you want to compare the relative stability of a bound ion pair versus an unbound one I think you're better off doing e.g. umbrella sampling. Peter On 10-03-17 04:48, #SUKRITI GUPTA# wrote: > Dear all, > > > I have two systems: 1. metal ion in

Re: [gmx-users] Question regarding coarse-graining martini

Hey Ali, 1) You usually can't use PR for equilibration - it'll oscillate out of control and blow up. What I usually do is use Berendsen for equilibration, and PR for the production run. 2) What do you mean exactly? The numbers mean the same, but I'm not sure of any physical effect as a result

Re: [gmx-users] Question regarding coarse-graining and all-atom structure

insane will make a new bilayer for you, not forward-map an atomistic one. Maybe backwards does what you want, although it's usually used in the other direction. http://cgmartini.nl/index.php/tools2/resolution-transformation Peter On 18-02-17 23:14, Justin Lemkul wrote: > > > On 2/18/17 2:39

Re: [gmx-users] MD simulation of peptide amphiphile using CG method

On 03-02-17 13:01, leila karami wrote: > Dear Peter, > > Thanks for your answer. > >> you'd best redirect this question to the Martini forum (cgmartini.nl), >> since this is more of a forcefield question than a Gromacs question. > You are right. At first, I asked my question in Martini forum,

Re: [gmx-users] MD simulation of peptide amphiphile using CG method

Hi, you'd best redirect this question to the Martini forum (cgmartini.nl), since this is more of a forcefield question than a Gromacs question. To answer your question: if at all possible, stick to the 36 Martini bead types available, and look at the tutorials on the Martini webpage. There's

Re: [gmx-users] Using backward.py with Gromacs 5.x?

Hi Srinivas, You're probably better off asking this on the Martini forum (cgmartini.nl). What I would suggest for now (as a quick fix) is to define bash aliases for grompp and mdrun, and have them point to gmx grompp and gmx mdrun respectively. There might be more subtle effects as well though.

Re: [gmx-users] gmx make_ndx: select last created group without knowing its number

Or, alternatively, use gmx select with the -sf and -on flags. Peter On 22-01-17 13:57, Mark Abraham wrote: > Hi, > > Sure, you can give and refer to groups either by name or number, so there > are many possible solutions for you. Easiest is to give it a name at the > time you make it, and then

[gmx-users] readline support for gromacs tools

Hi all, does Gromacs use the GNU readline library, so that I may "navigate" in the commands I give to e.g. gmx select using the arrow keys? Or did I do something wrong in my compilation? Cheers, Peter p.s. cmake .. -DCMAKE_INSTALL_PREFIX="/usr/local/$VERNAME" -DGMX_X11=ON

Re: [gmx-users] How to choose z component of two groups

Hi, it's probably easier to get the membrane thickness using `gmx density`. Peter On 09-01-17 11:58, Mijiddorj Batsaikhan wrote: > Dear gmx users, > > I am performing analysis of membrane system. I would like to estimate > membrane thickness. > > I toke following command: > > gmx distance 0s

Re: [gmx-users] Gromacs Simulation Question

On 07-01-17 21:12, Justin Lemkul wrote: > > > On 1/6/17 5:14 PM, Academic Research wrote: >> Hello everyone, >> >> >> I have computationally designed several synthetic proteins that are >> not found in >> nature. >> >> >> My lab has limited resources for wet lab work and so I would like to >>

Re: [gmx-users] CG Lincs errors

As a note to Alex (and the rest of the list), the coarse-grained Martini forcefield is usually run with timesteps between 20-40 fs. 15fs is already rather low. I do agree that longer equilibration at low timestep (5 or 10) might help. Alternatively, Do you think a semiisotropic pressure coupling

Re: [gmx-users] Computer processor and graphics card choice

Hi Guille, I'm not an expert on this, but it'll also depend on what kind of MD simulations you want to run. Coarse-grained forcefields, for example, don't benefit much from a GPU. So what kind of simulations do you have in mind? Atomistic? QM/MM? How many particles? ...? Peter On 02-12-16

Re: [gmx-users] Neighbor searching artifacts in permittivity when using shift

Hi Julian, unfortunately I can't answer you question regarding the neighbour search algorithm. However, it should be noted that there are alternative mdp parameters available for Martini using the Verlet cutoff-scheme, made specifically for gromacs 5. Would you be willing to try those? You can

Re: [gmx-users] pressure coupling

Hi, IIRC you can set pcoupl to semiisotropic, set the x/y compressibility (or tau-p?) to 0, and set z to what you want it to be. Peter On 17-10-16 21:45, pari lotfi wrote: > Dear all, > > How can I simulate a box of water in NATPz condition? > In this simulation, particle number N, surface

Re: [gmx-users] Regarding tc-grps

Hi, please see http://www.gromacs.org/Documentation/Terminology/Thermostats The number of molecule types (what you call groups?) in your .top file are not relevant for the number of tc groups you make. You need to make sure your system obeys a boltzmann distribution (or maxwell? I'm not sure).

Re: [gmx-users] Fwd: is there martini CG parameters for K+ ion?

Hi, disturbing to hear you can't register on our forums. We've been having some trouble with the website, so we'll definitely look into it. As for the science: Na+ and K+ are identical in Martini. The size difference is compensated by the implicit solvation shell anyway. You'd have to look into

Re: [gmx-users] solvating hexagonal biphasic system

Hi Neha, If I recall correctly, you can represent any periodic system as cubic - and this is what Gromacs uses internally. Peter On 05/08/16 05:42, Neha Gandhi wrote: > Dear list, > > I am trying to build a system with HAP and a protein. I was able to insert > protein 10nM above the

Re: [gmx-users] [pairs] vs [exclusions]

the same atoms, to > show the total energy restored, but now in a different component. > > Mark > > On Wed, Jul 13, 2016 at 4:04 PM Peter Kroon <p.c.kr...@rug.nl> wrote: > >> Hi Xavier (and list), >> >> I think that's a good way of rephrasing my question ;) >&g

Re: [gmx-users] [pairs] vs [exclusions]

sion act on the regular LJ and pairs add a different > LJ(14)? > > With exclusions, do you have the regular LJ present? > > XAvier. > >> On 13 Jul 2016, at 13:17, Peter Kroon <p.c.kr...@rug.nl> wrote: >> >> Hi Mark (and list), >> >> thanks for the ideas. >&

Re: [gmx-users] [pairs] vs [exclusions]

r life > easier by playing around with atoms with high indices. > > Mark > > On Wed, Jul 13, 2016 at 10:46 AM Peter Kroon <p.c.kr...@rug.nl> wrote: > >> Dear list, >> >> I a have a short question on topologies, and the manual is somewhat >> unclear. >>

[gmx-users] [pairs] vs [exclusions]

, or not? Thanks in advance, Peter Kroon PS. short example topology: [ moleculetype ] my_molecule 1 [ atoms ] ... [ pairs ] 1 4 2 . [ exclusions ] 1 4 [ bonds ] no bond between 1 and 4 ... -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] gromacs command in mpi single precision

Hi, my personal solution to this is to tell mpirun to run 'gmx_mpi grompp' just once on just one cpu: `mpirun -n1 -c1 gmx_mpi grompp ...`. But like Mark wrote, it depends on your installed MPI whether this is needed. Peter On 29/06/16 10:49, Mark Abraham wrote: > Hi, > > The MPI build only

Re: [gmx-users] questions related to md.mdp

Hi, On 06/04/16 10:22, Brett wrote: > Dear All, > > Based on the on-line lysozyme tutorial, > > the first several lines I used for my md.mdp was as following, > > title= OPLS Lysozyme MD > ; Run parameters > integrator= md; leap-frog integrator > nsteps= 500;

Re: [gmx-users] pull code in 5.1.2

Hi, According to the manual (http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html#com-pulling) it should be something like this: pull = yes pull-nstxout= 1000 pull-nstfout= 1000 pull_ngroups = 1 pull_group1_name = JON_SNOW_KNOWS_NOTHING pull_ncoords = 1

[gmx-users] AIREBO and multibody non-bonded potentials in GROMACS

Dear list, I need to model disulfide exchange reactions in an efficient way. A literature search turned up the AIREBO formalism postulated by Brenner at al[1]. I would like to implement this in Gromacs 5.1 as a non-bonded functional form which has an angle dependence. So, my questions: 1) Has

Re: [gmx-users] g_tcaf use issue

On 11/11/15 03:16, Jones de Andrade wrote: > Hello. > > We are using gromacs in order to explore how well/not so well different > methods to calculate dynamical properties of liquids perform. > > At this moment, we are using g_tcaf (already seen g_energy -visc results) > to evaluate how it would

Re: [gmx-users] Definition in martini CG force field

Hi Sara, first off, you're probably better off asking these Martini-specific questions on the Martini forum (cgmartini.nl) Secondly, some answers are inline On 11/11/15 10:57, mohammad agha wrote: > Dear Gromacs users, > May I ask you to help me, Please? > 1- I want to run the system with

[gmx-users] AIREBO and multibody non-bonded potentials in GROMACS

Dear list, I need to model disulfide exchange reactions in an efficient way. A literature search turned up the AIREBO formalism postulated by Brenner at al[1]. I would like to implement this in Gromacs 5.1 as a non-bonded functional form which has an angle dependence. So, my questions: 1) Has

Re: [gmx-users] Turning off nonbonded interactions in protein-DNA

gmx dump -s my_run.tpr should give you all the information you need. On 23/10/15 07:43, Kartheek wrote: > Dear all, > I am trying to do a simulation of protein-DNA complex by turning off all > nonbonded interactions between protein and DNA, as suggested in the mailing > list an "exclusions"

Re: [gmx-users] "The sum of the two largest charge group radii is larger than rlist"

In addition, aren't tpr's made with gromacs 5 compatible with gromacs 4? Peter On 13/10/15 14:04, Justin Lemkul wrote: > > > On 10/13/15 8:01 AM, Shima ebrahimi wrote: >> >> >> Dear users, >> >> I want to calculate binding free energy with g_mmpbsa in Gromacs 4.5 but >> my trajectory has been

Re: [gmx-users] GPU installation of gromacs:Tesla K20c

1) put `source /usr/local/gromacs/bin/GMXRC` in your ~/.bashrc file. 2) Type `echo $PATH` and make sure you find your path to Gromacs in there. 3) try `gmx mdrun`. Im not sure whether that is already required for Gromacs 5.0.5. Also, have a look in /usr/local/gromacs/bin to see whether 'gmx',

Re: [gmx-users] problem with gpu performance

> At this point, we have two plans: either go for single 4 GB GTX-970 or two > 2 GB GTX-960 . I was wondering whether you can comment on which options > will be better as far as performance is concerned. > Thanks for your input > jagannath > > On Fri, Sep 4, 2015 at 6:45 PM,

  1   2   >