Re: [gmx-users] anyone have a development version or fork of gromacs that puts bonded interactions on the GPUs?

tly increase performance in Martini simulations, perhaps not quite as much as all-atom simulations but typically at least ~2x the speed of the same system on cpus alone. What combination of gromacs version/mdp options/hardware are you running with? Kevin On Thu, Apr 5, 2018 at 3:10 PM, Chris

Re: [gmx-users] Regarding calculation of Spatial Distribution Function

Mark addressed your second post. Regarding your first post, it looks like that program help output was mangled somewhere between 4.6.5 and 5.1.2. Below is the output from g_spatial in gromacs 4.6.5, which should give you an idea of what the help output should say (e.g. use a .xtc input file and

[gmx-users] anyone have a development version or fork of gromacs that puts bonded interactions on the GPUs?

Hello, running Martini simulations with gromacs does not dramatically benefit from the presence of GPUs, presumably because the bonded interactions on the CPUs is the bottleneck. Does anyone have even an untested hacky version of gromacs with bonded pushed to the GPUs? PME is not used so that

[gmx-users] cudaMallocHost filed: unknown error

Hello, I am running gromacs 5.1.2 on single nodes where the run is set to use 32 cores and 4 GPUs. The run command is: mpirun -np 32 gmx_mpi mdrun -deffnm MD -maxh $maxh -dd 4 4 2 -npme 0 -gpu_id -ntomp 1 -notunepme Some of my runs die with this error:

[gmx-users] MPI-specific compile problem finding fftwf_plan_r2r_1d in libfftw3f.a -- undefined reference to `_intel_fast_memset'

Hi, I resolved the issue. I forget to use -DGMX_MPI=ON , though fixing that did not resolve the issue. The issue appears to be that the intel mpi compilers are not called mpicc and mpicxx so I was mixing things in a strange way that happened to cause problems with fftw loading. The

Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

1) take one of your systems, repeat the setup with different random seeds, run another 20 ns and make the RDF 2) post the two RDFs of different runs with the same concentrations here: http://photobucket.com/ 3) reply to this list with a link to your image and explain what it is about your

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

r 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 pretty easy, I use gmx trjconv -b and -e to get the part before > the corruption and the part after the corruption, whi

Re: [gmx-users] Constant Pressure just in z axis

I set the pressure the same. Not sure if it matters or not. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Iman Ahmadabadi Sent: 05 October 2017 03:16:01 To:

Re: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

Please show us the plots (upload to a file hosting site and paste the link in your post) or precisely define your results; also explain precisely why the results are unexpected. Also show us your exact commands. Without this we can not help. From:

Re: [gmx-users] Constant Pressure just in z axis

Use semi-isotropic pressure coupling and use a water-type compressibility in the z dimension by a compressibility of 0 in the x/y dimension. That will give you precisely what you are looking for. We've used it before to simulate octane slabs as lipid bilayer mimetics and it work just fine.

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

Dear users: I recently experienced some corruption in a .xtc and a .edr file. Recovering the .xtc was pretty easy, I use gmx trjconv -b and -e to get the part before the corruption and the part after the corruption, which was itself a small chunk. This presumably works because trjconv

Re: [gmx-users] TIP4P/ice pdb file

I believe that you can use any 4-point water model .gro for any 4-point water topology (or likewise for 3-point water models). Did you try it yet? If so, what problem are you running into specifically? From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] Errors during pull constrained NPT simulation for permeability calculations.

Dear Yogesh: you either need to make the system larger in the dimension(s) of your pulling or you need to not pull out to such a far distance. Once you straighten that out, and if the lincs problems remain, then we can tackle that separately. What are your mdp options for pulling? Maybe you

Re: [gmx-users] Output center of mass of each molecules in a system.

make an index file with gmx make_ndx and then script it to create an index for each water molecule, e.g.: gmx make_ndx -f my.gro -o index.ndx << EOF $(for((i=1;i<=100;i++)); do echo r${i}; done) q EOF then you can likewise script the input to gmx traj

Re: [gmx-users] gmx trjconv -center -boxcenter zero isn't amazing at putting the selection at (0, 0, 0), but I don't know why

the behaviour I need. Thank you, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Christopher Neale <chris.ne...@alum.utoronto.ca> Sent: 01 June 2017 15:58:58 To: Discussion list

Re: [gmx-users] AMBER LIPID14 ff in GROMACS

Possibly build in amber and then convert to gromacs input format with parmed: https://github.com/ParmEd/ParmEd/issues/631 Looks like it might be a little tricky and of course you'd want to compare single-point energied in amber and then in the gromacs port, though that is complicated by code

[gmx-users] gmx trjconv -center -boxcenter zero isn't amazing at putting the selection at (0, 0, 0), but I don't know why

Dear Users: Using gmx 5.1.2, I find that centering a selection of the system at (0,0,0) works better via "editconf -c -center 0 0 0" than it does via "trjconv -center -boxcenter zero" here's the comparison of the center of mass of the selection centered in these two different ways: TRJCONV:

Re: [gmx-users] please help clarifying units for potential energy and enthalpy from gmx energy

s for some reason the desired behaviour. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Christopher Neale <chris.ne...@alum.utoronto.ca> Sent: 30 May 2017 23:25:46 To: Discussion

Re: [gmx-users] System volume "jumps" on exact continuations

1. Once you identify a continuation (with associated run script) that gives the discontinuity, if you run many repeats of the original continuation then does the jump always occur or only sometimes? 2. Did you do any of the MPI runs with -notunepme ? That would be my first suspect. 3. Did

[gmx-users] please help clarifying units for potential energy and enthalpy from gmx energy

Dear Users: I am trying to figure out what “potential energy” and “enthalpy” really mean in the output from gmx energy. It took me a while to realize that even when the (more hidden than it should be) option -nmol is not used and therefore is set to its default value of 1, the .xvg output

Re: [gmx-users] Regarding simulation radioactive material

Unless you're using a bizarre Hamiltonian that includes mass then you should be able to change masses without affecting equilibrium thermodynamic properties at all, right? Dynamics will of course be altered. Justin's right though, any thermodynamic differences in C14 vs C12 would have to be

[gmx-users] gmx cluster -binary flag to get the "centroid" as the member that has max neighbours < cutoff ?

Dear users: I have a bunch of trajectories of the same system. I want to cluster them together (using gmx cluster gromos algorithm), identify the centroids, and then use gmx rms to evaluate the RMSD to the centroid of the top N clusters in each trajectory. The reason I want to do this is to be

Re: [gmx-users] mixed 1-4 scaling factor

In reply to Mark's comment, it used to be that one could specify separate LJ 1-4 interactions as he suggests, but there is no route to do this for Coulmb 1-4 scaling. Perhaps that haas changed in more recent versions of gromacs. If not, you might consider a variant of the approach that we used

[gmx-users] (Opt.) indication to gmx cluster -s doesn't seem to be optional

Dear users: I'm writing to check that I understand the "(Opt.)" notification in gmx * -h output. For example, gmx cluster -h lists a topology as optional: -s [<.tpr/.gro/...>] (topol.tpr) (Opt.) But without a topology the evaluation crashes: GROMACS: gmx cluster,

Re: [gmx-users] Reply To: Fatal Error - XTC error - maybe you are out of disk space?

If Justin's right, then you should be able to solve the problem by saving less frequently (xtc, edr, cpt, trr). If you're running on a laptop and overwhelming the hard drive bandwidth, then I can almost guarantee you're saving 100x more than you need to for most systems. Unless you have a very

Re: [gmx-users] Higher that usual salt bridge occupancies in Amber99sb*-ildn forcefield despite adding nonbonded corrections

Just to list the ways that such a thing could happen: 1. change to $GMXLIB 2. change to the version of gromacs you are using or just a change to a different installation (so you have a different top directory) 3. you automate grompp by piping in a number and some change to #1 or #2 above has

Re: [gmx-users] Replica exchange simulations more than number of processor

drophobicity at the lower lambda's? I've seen this selective scaling work well in other types of system to counteract broadly similar types of sampling issues at lower lambda's. Just a thought, it might not work well for what you are doing, Cheers Tom On 14/04/17 19:27, Christopher Neale wrote

Re: [gmx-users] Replica exchange simulations more than number of processor

6 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Replica exchange simulations more than number of processor Hi Chris, This is interesting. Do you have an idea why the sampling at low lambda values isn't very good? Cheers Tom On 14/04/17 17:40, Christopher Neale wrote: > What I have is only

Re: [gmx-users] Error In Umbrella sampling.

Yup, I use maxwarn all the time in that case. It's safe for general usage. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Anurag Dobhal Sent: 14

Re: [gmx-users] Replica exchange simulations more than number of processor

ssor On Fri, Apr 14, 2017 at 5:51 PM, Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Just my 2 cents: REST2 doesn't work. The random walk is much better than > REST but the sampling efficiency at low lambda is now poor. Interesting. Is there any (published) data you coul

Re: [gmx-users] Fatal Error - XTC error - maybe you are out of disk space?

Is this on your personal laptop or on a cluster? On a cluster, perhaps you have hit your user or group quota for file size or number of files (especially if you are running in $HOME or something). I have also seen this when there really should be space available, but the issue was (again on a

Re: [gmx-users] Replica exchange simulations more than number of processor

Just my 2 cents: REST2 doesn't work. The random walk is much better than REST but the sampling efficiency at low lambda is now poor. Your mileage may vary, but be aware that REST2 is not necessarily going to be useful for all systems. From:

Re: [gmx-users] Density calculation

You have not really defined what you want to obtain all that well. E.g. a mass density is mass per volume, but you seem to take issue with the volume definition. Do you just want to know the mass density in a region that is near the center of your cellulose? If so, you could use gmx traj to get

[gmx-users] mdrun (5.1.2) restart doesn't recognize pull-code files given default but unspecified names

Dear users: I noticed some unexpected behaviour with gromacs 5.1.2 and wanted to check here first if it's known and fixed in later versions, or if people consider this behaviour to actually be desirable, before posting a redmine. It's a minor issue. The behaviour might be desirable, since the

Re: [gmx-users] importance of nvlink in GPU nodes?

NVLINK in GROMACS. The 2018 release might make some > use of it. > > Mark > > On Wed, Mar 29, 2017 at 4:19 AM Christopher Neale < > chris.ne...@alum.utoronto.ca> wrote: > > > Dear users: > > > > does anybody know if the presence of either CPU-to-GPU o

[gmx-users] importance of nvlink in GPU nodes?

Dear users: does anybody know if the presence of either CPU-to-GPU or GPU-to-GPU nvlink affects the performance or efficiency of gromacs? Thank you, Chris. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

[gmx-users] gmx cluster without allowing Z-rotation?

Dear users: does anybody know if a simple code modification will permit gmx cluster to do the fitting while allowing translation in X, Y, and Z but rotation only in X and Y? I'm trying to do structural clustering on a membrane protein where tilt may be an important feature so I don't want to

Re: [gmx-users] Problem with obtaining rational Area per lipid

5 ns is not long enough to equilibrate the APL, and it's a time-averaged property in experiment, so looking at one frame is not as good as averaging over tens of ns of simulation. Try running for 100 ns and taking the average of the last 50 ns. Also, what APL do you get and what value do you

Re: [gmx-users] Radial distribution function for larger distances

gromacs default units in nm, not Angstroms. I doubt you have a useful RDF up to only 1.8 A. In any event, if you are running into a distance beyond which you can not make a useful RDF, then it is likely an issue with box size, not mdp options. From:

Re: [gmx-users] Radial distribution function for larger distances

It's unclear what your issue is. I presume you are concerned that the rdf might not be valid at distances longer than your cutoff? In that case, adding dispersion correction might be something to think about, but then again that will depend on the force field and the system too. Unless I'm

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

I believe it is like this time x1 y1 z1 x2 y2 z2 ... xN yN zN so you want to average like this: cat thickness.xvg | grep -v '[#|@]' | awk '{s=0;for(i=4;i<=NF;i+=3){s+=$i;n++};avg=s/n;print $1,avg}' Obviously do a sanity check on the output. Still, I agree that the comments at the top of

Re: [gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

think it should. We're very happy to make things work better! > > Mark > > On Mon, 6 Feb 2017 10:04 Kroon, P.C. <p.c.kr...@rug.nl> wrote: > > > Alternatively, center it on an interfacial residue. pbc cluster doesn't > > always work, unfortunately. > > > >

Re: [gmx-users] modelling of calcium ions

The things you'll have to be most careful of include whether the calcium ion parameters you choose can get the correct coordination states (as I recall, Calcium's coordination can be quite variable experimentally, in contrast to something like magnesium, which has a more strict coordination

Re: [gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

ise changing atomic coordinates Hi, I've never really use it myself, but I imagine trjconv -pbc cluster is useful for this kind of scenario when you want to treat a group of molecules as indivisible. Mark On Sat, 4 Feb 2017 09:33 Christopher Neale <chris.ne...@alum.utoronto.ca> wrote: &

[gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

Dear users: I have a system in which molecule A is in direct contact with molecule B. However, molecule B is imaged in a different periodic cell. What I would like to do is to get an image of both molecules in a periodic representation in which they actually are in contact (i.e., reimage

Re: [gmx-users] 'conditional' pull during MD simulation

Try gromacs with the plumed plugin ( http://www.plumed.org ). They have their own mailing list, so you can ask there, but I suspect that most things you want to do can be done that way. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] how to arbitrarily increase the XY size of an existing bilayer system (adding more lipids)

more lipids) What about tilling 2x2 and then removing lipids that have x larger than a cutoff … then minimisation+equilibration of the interface even atomistic would be quite trivial. X- > On 01 Feb 2017, at 17:14, Christopher Neale <chris.ne...@alum.utoronto.ca> > wrote: > &g

Re: [gmx-users] how to arbitrarily increase the XY size of an existing bilayer system (adding more lipids)

/02/17 16:14, Christopher Neale wrote: > Dear Users: > > I have some atomistic systems of a membrane protein embedded in a lipid > bilayer. I currently have N lipids and I would like to increase that to 1.5N > or 2N lipids (distributed equally in the bilayer plane) without disturbin

[gmx-users] how to arbitrarily increase the XY size of an existing bilayer system (adding more lipids)

Dear Users: I have some atomistic systems of a membrane protein embedded in a lipid bilayer. I currently have N lipids and I would like to increase that to 1.5N or 2N lipids (distributed equally in the bilayer plane) without disturbing the existing structure. Increasing to 4N lipids would be

[gmx-users] Protein-surface interaction during flow

-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Christopher Neale Sent: Tuesday, January 31, 2017 11:15 AM

[gmx-users] Protein-surface interaction during flow

flow the solvent and let the protein respond freely to that? My guess is that the initial velocities will be lost fairly quickly to thermal noise if you try the suggestion of giving it a kick and then simply letting it go. — original message — I am trying to simulate a flow of protein over

[gmx-users] Pulling ligand out of protein for umbrella sampling

Suhaib Shekfeh 12 days ago ReplyPermalinkRaw Message Dear GMX-users In an old post in this list about umbrella sampling in gromacs and the pull code, ( http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/w3NmJ69y/md-pull-code-in-umbrella-sampling ) Christopher Neale gave an interesting

[gmx-users] g_spatial Problem

Dear Sakiru: This topic was discussed before on-list: https://www.mail-archive.com/search?l=gromacs.org_gmx-users@maillist.sys.kth.se=subject:%22%5Bgmx-users%5D+g_spatial%22=newest=1 Basically, if you have 48 molecules of A, then you need to process your trajectory so that it is 48x larger in

[gmx-users] gmx spatial

Dear Hoda: You’re likely seeing water mostly on one side because of PBC. I suggest you modify your commands such that you create a new .gro file in which the protein is centred and PBC is re-imaged (trjconv -center -pbc mol) and then use that to create a new .tpr file and then use that new

Re: [gmx-users] trjconv sampling according to a list of arbitrary times

I don't know how to do exactly what you want to do, but you can at least do this so that trjconv doesn't seek from the beginning of the file, it should speed things up a lot: for t in 1 20 220 620; do let b=$t-10 gmx trjconv -dump $t -b $b ... done Anyway, Mark's suggestion is much better

Re: [gmx-users] PMF decompostion

PMF gives free energy, which can not be decomposed into VDW and Q without leaving a remainder, though I guess that doesn't affect your question. Enthalpy is simply the average potential energy plus the pressure volume component. So you can compute average potential energy VDW and Q components

Re: [gmx-users] Removal of Waters in Hydrophobic Core

pent with my situation. Regards, *Sanim Rahman* B.S. Chemical Engineering, 2019 Undergraduate Researcher, Global Center for Hearing and Speech Research <https://www.linkedin.com/pub/sanim-rahman/108/a64/986> On Mon, Nov 28, 2016 at 9:11 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >

Re: [gmx-users] gmx distance -- gmx: double free or corruption

e reproduces it, then that would likely be best. I see you've tried to use -sf to simplify common subexpressions - that's likely a good idea in general. See e.g. gmx help selections evaluation. Mark On Fri, Nov 25, 2016 at 8:45 PM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Plea

Re: [gmx-users] Removal of Waters in Hydrophobic Core

On Sat, Nov 26, 2016 at 3:36 PM, Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > I have not run that in a long time, but looking at it (and my initial post > here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx- > users/2006-May/021526.html ) it seems like I wro

Re: [gmx-users] Poor sampling in PMF at some points

Most likely is that you have a very unfavorable position there. If so, the solution would be to add some umbrellas in that range that employ stronger force constants. However, before you do that, maybe try to run wham again with a larger bin width (large as you need to get an output PMF) and

Re: [gmx-users] Removal of Waters in Hydrophobic Core

Research On Fri, Nov 25, 2016 at 3:48 PM, Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > not sure if it is a typo or perhaps a command structure I am unfamiliar > with, but I don't understand your command. > > Try this: > > chmod +x keepbyz.pl > ./keepbyz.

Re: [gmx-users] The time need for each window in umbrella sampling

block averaging or perhaps reverse cumulative averaging http://scitation.aip.org/content/aip/journal/jcp/120/6/10.1063/1.1638996 (though the later will probably be a pain with PMFs). From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] setting up a pull vec

You haven't told us what you want to do, but perhaps you want to pull them apart along the vector that connects the centers of mass of these two species. One possible way to do that is to use gmx traj -com to get the two centers of mass, then figure out the vector yourself. That's going to get

Re: [gmx-users] Removal of Waters in Hydrophobic Core

not sure if it is a typo or perhaps a command structure I am unfamiliar with, but I don't understand your command. Try this: chmod +x keepbyz.pl ./keepbyz.pl new_waters.gro > keep_these_waters.gro see here: http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations?highlight=generates

Re: [gmx-users] gmx distance -- gmx: double free or corruption

. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Christopher Neale <chris.ne...@alum.utoronto.ca> Sent: 25 November 2016 14:33:51 To: Discussion list for GROMACS users Subject: [gmx-users] gmx dis

[gmx-users] gmx distance -- gmx: double free or corruption

Dear Users: I am having trouble with gmx distance crashing in gromacs 5.1.2. I am trying to analyze the distance of different peptide residues from the center of a lipid bilayer. have CA atoms on residues 2-20 and also on residues 22-40 (2 peptides). If I try to do residues 2-20 it works fine.

Re: [gmx-users] Unable to compile plug-in support for gromacs 5.1.2

a libgromacs with some statically-linked dependencies has to be incapable of having a dynamically loaded function, but our CMake implementation probably assumes it for simplicity. Mark On Wed, Nov 23, 2016 at 10:01 PM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > All

Re: [gmx-users] Unable to compile plug-in support for gromacs 5.1.2

sers] Unable to compile plug-in support for gromacs 5.1.2 Hi, Offhand the first error is inexplicable, but the first is that the linker flags aren't set up right. However I do think we fixed that at some stage... Mark On Wed, 23 Nov 2016 21:23 Christopher Neale <chris.ne...@alum.utoronto.ca&

Re: [gmx-users] Melting temperature for the lipid bilayer

in gel phase. Cheers On Wed, Nov 23, 2016 at 12:28 PM, Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > I presume you're heating your bilayer up slowly to assess the melting > temperature? This method will give you an estimated melting temperature > that is equal to t

Re: [gmx-users] Unable to compile plug-in support for gromacs 5.1.2

problem (and same thing if I used -DCMAKE_INCLUDE_PATH=/usr/include as a cmake argument). Thanks again for any help, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Chris

Re: [gmx-users] Melting temperature for the lipid bilayer

I presume you're heating your bilayer up slowly to assess the melting temperature? This method will give you an estimated melting temperature that is equal to the true melting temperature of that Hamiltonian in simulation only if you go infinitely slowly. At finite heating speeds, your observed

[gmx-users] Unable to compile plug-in support for gromacs 5.1.2

Dear Users: I tried to compile gromacs 5.1.2 with plugin support, but upon running gmx trjconv I get the following error message indicating that plugin support was not actually included: $ /scratch/cneale/exe/GROMACS/exec/gromacs-5.1.2/serial_plugins/bin/gmx trjconv -f MD1.mdcrd.nc -s EM.gro

Re: [gmx-users] high-temperature MD

Depends, actually. There are reasons one might want to simulate a system at 380 K in NVT using the average box volume from the 300 K NPT simulation. Temperature replica exchange typically employs NVT and so might other temperature-based enhanced sampling approaches. Justin's right, you have to

Re: [gmx-users] g_spatial Problem

edin <abedi...@husky.neu.edu> Sent: 05 October 2016 15:58:14 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] g_spatial Problem Dear Dr. Neale, Please find the following link of dropbox that contains the files. https://www.dropbox.com/sh/ifeaegequznnbgg/AABO9AzE3PrbNtGfgMike0tWa?dl=0 Pl

Re: [gmx-users] g_spatial Problem

Can you please describe the system a bit more (especially how many molecules of each of the 4 types you have) and also provide more information about what you want to obtain (sdf, obviously, but of what and ideally also why). 1. your procedure could be ok, but also maybe not. Depends on what

Re: [gmx-users] LINCS warnings at high temperature md run

Try adding "lincs-order = 6" to your mdp file. The following settings don't give me lincs warnings at 500 K, though I presume that the lincs-order is the essential part. constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs dt = 0.002 integrator = sd tc_grps

[gmx-users] how likely that charmm-in-gromacs LJ-14 interactions are affected by inclusion of cgenff stuff when adding a new molecule with published charmm parameters?

Dear Justin: I have another question, this time about LJ 1-4 interactions. I notice that charmm36-jun2015.ff/ffbonded.itp has the following in [ pairtypes ] NH1 S 1 0.316269044940 1.2552 and it has the following in [ atomtypes ] S1632.060.000 A

Re: [gmx-users] charmm36 gromacs/charmm simulation package gives different electrostatic energies with same charges (probably I am using charmm incorrectly)

s different electrostatic energies with same charges (probably I am using charmm incorrectly) On 8/7/16 2:21 AM, Christopher Neale wrote: > Dear Gromacs users: > > This is a hybrid gromacs/charmm question, but there is not such a mailing > list and I am hoping this is a suitable place f

Re: [gmx-users] charmm36 gromacs/charmm simulation package gives different electrostatic energies with same charges (probably I am using charmm incorrectly)

lectrostatic energies with same charges (probably I am using charmm incorrectly) On 8/7/16 2:21 AM, Christopher Neale wrote: > Dear Gromacs users: > > This is a hybrid gromacs/charmm question, but there is not such a mailing > list and I am hoping this is a suitable place for this q

[gmx-users] charmm36 gromacs/charmm simulation package gives different electrostatic energies with same charges (probably I am using charmm incorrectly)

Dear Gromacs users: This is a hybrid gromacs/charmm question, but there is not such a mailing list and I am hoping this is a suitable place for this question. I am trying to convert some charmm36 parameters (from a new paper) to gromacs format and for this I am doing single-point energy

[gmx-users] mpirun -npernode option gives gromcs slowdown unless used with mpirun option -np or gromacs option -ntomp 1

Dear Users: this is simply an informational post in case somebody runs into similar troubles in the future. I don't understand why the usage must be this way, but empirically it works. I find that when I use (A) "mpirun -np 4 gmx_mpi -ntomp 6" I get 32 ns/day. However, if I instead use (B)

[gmx-users] Gromacs and Software RDMA over Converged Ethernet -- is there a point ?

Dear Gromacs users: I have access to a new cluster that has GigE interconnect (selected vs. IB for reasons other than cost). As expected, systems that scale nicely to two nodes with IB end up running faster on 1 node than they do in 2 nodes when using GigE. SysAdmins are wondering if software

Re: [gmx-users] PMF steadily increasing

gt; 2016-06-15 19:01 GMT+02:00 Christopher Neale <chris.ne...@alum.utoronto.ca > >: > >> (1) Are the protein and peptide really never interacting at d=7 nm? I >> presume you've got a peptide that would be maybe 5 nm long when fully >> extended, and your dG minimum is at 1.5 nm, so

Re: [gmx-users] compile 2016-beta2 failed

cicc is a cuda compiler (i.e., nvcc) From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Albert Sent: 17 June 2016 14:55:02 To: gmx-us...@gromacs.org Subject: Re:

Re: [gmx-users] Basic Understanding about Gromacs C library

Writing your own analysis tool in template.c might not be the best solution either. You have to worry about things like pbc breaking and you in many cases need to write routines that already exist elsewhere. I suggest looking into standalone analysis kits such as http://loos.sourceforge.net/ or

Re: [gmx-users] PMF steadily increasing

(1) Are the protein and peptide really never interacting at d=7 nm? I presume you've got a peptide that would be maybe 5 nm long when fully extended, and your dG minimum is at 1.5 nm, so giving half the peptide length that would imply possible contact at 4 nm, so I expect 7 nm is sufficient,

Re: [gmx-users] Lipid parameterization

om: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 14 June 2016 14:35:26 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Lipid parameterization On 6/14/16 2:04 PM, Christopher Neal

Re: [gmx-users] Lipid parameterization

You might see if CHARMM_GUI has parameters for it. This is not to say that they will be amazing parameters, as I have not looked into their approach to generate parameters and it may well be rational cut and paste, but they do have parameters for loads of lipids. If they don't have parameters,

Re: [gmx-users] Decreased Area/Lipid of Lipid Bilayer from CHARMM-GUI

ithm = LINCS continuation = yes ; nstcomm = 100 comm_mode = linear comm_grps = MEMB SOL_ION ; refcoord_scaling = com Thanks, Nidhin Thomas University of Houston > Message: 4 > Date: Mon, 13 Jun 2016 17:51:43 + > From: Christopher Neale <chris.ne...@alum.utoronto.ca> &

Re: [gmx-users] water density

I am fairly confused about what you want to obtain and what you have done, but is it possible that you simply have not turned on pressure coupling? General procedure even if you eventually want to do constant volume simulation is to do some equilibration with constant pressure to get densities

Re: [gmx-users] Decreased Area Per Lipid for Lipid Bilayer obtained from CHARMM-GUI

In future posts, it is best to copy and paste your .mdp file because we can not all get attachments from the list. Regarding your results, it is my understanding that the CHARMM-GUI has parameters for, and can build, many lipids systems whose parameters have not been completely validated by

Re: [gmx-users] problem about distance restraint in REMD simulation

This is essentially what I have done and it worked fine for me. In fact, not being as clever as Mark I simply commented out that entire if/gmx_fatal block of code and use this modified code only in cases where I an not concerned about other side-effects. It is stable for >500 ns/replica.

Re: [gmx-users] Analyse REMD

Dear Ouyang: There is a script in the gromacs package (at least up to 5.1.2) called demux.pl . You can use it to get more human friendly information out of your REMD runs ( see http://www.gromacs.org/Documentation/How-tos/REMD for some very sparse info on demux.pl ). Basically you feed it the

Re: [gmx-users] Combining various Flat-bottomed Potentials

-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 24 May 2016 12:33:54 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Combining various Flat-bottomed Potentials On 5/24/16 12:30 PM, Christopher Neal

Re: [gmx-users] Invalid selection near '&' syntax error -- easy way to avoid?

s.kth.se> on behalf of Teemu Murtola <teemu.murt...@gmail.com> Sent: 20 May 2016 23:33:36 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Invalid selection near '&' syntax error -- easy way to avoid? Hi, On Sat, May 21, 2016 at 1:09 AM Christopher Neale < chris.ne...@alum.utoront

Re: [gmx-users] Combining various Flat-bottomed Potentials

I doubt it. The flat-bottom potential in the pull-code is not really the standard definition of a flat-bottom potential. In my opinion, a flat-bottom potential has a low, and a high defined value and then the restraint increases harmonically above high and below low with no penalty between low

Re: [gmx-users] Invalid selection near '&' syntax error -- easy way to avoid?

sn't immediately do want you want, then gmx select is much more powerful. The former is not going to get enhanced given that the latter exists. Mark On Sat, 21 May 2016 00:14 Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/20/16 5:54 PM, Christopher Neale wrote: > > Dear Us

[gmx-users] Invalid selection near '&' syntax error -- easy way to avoid?

Dear Users: I find that gmx make_ndx will create groups with names that have ampersands in them and that this complicates piping the group name back into an analysis tool. I have included an example below. There is an obvious solution with sed to rename the group in the .ndx file after

[gmx-users] make_ndx treats "&" and "AND" differently -- expected?

Dear Users: In an attempt to get around the '&' issue in index group names, I have tried using the 'AND' keyword, which is noted in the gmx make_ndx -h output. Indeed, the word "AND" replaces the ampersand in the index group in this case. However, the selection seems broken to me. Details are

Re: [gmx-users] OPLS problem

old <steve...@ymail.com> Sent: 20 May 2016 13:37:01 To: Christopher Neale Subject: Re: [gmx-users] OPLS problem Thanks Christopher I was using, as it is recommended, TIP4P. When I switched to TIP3P I no longer get the error. So what do I do if I want to use TIP4P? Steve On Friday, May 2

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