[gmx-users] dx2_pbc() function and BOX_MARGIN

is: why test BOX_MARGIN*d2new instead of simply d2new? The comment where BOX_MARGIN is #defined mentions only testing for far too skewed boxes. Thanks, -- Elton Carvalho -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List b

Re: [gmx-users] Building a Larger Liquid Phase - Truncate 'Vacuum'

ting one domain per thread (be it OpenMP or MPI). Thanks. -- Elton Carvalho -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)

Re: [gmx-users] Building a Larger Liquid Phase - Truncate 'Vacuum'

gt; > There is no use of DD in this case. > Thanks, Justin, If there's no DD if only OpenMP threads are used, how is the load distributed among the threads? Particle decomposition? If I issue the option -dd X Y Z will it be ignored if there's one oen (thread-)MPI process? -- Elt

Re: [gmx-users] Building a Larger Liquid Phase - Truncate 'Vacuum'

ode. Thanks, Justin! >> option -dd X Y Z will it be ignored if there's one oen (thread-)MPI >> process? >> > > You'd probably get a fatal error. > Makes sense. Thanks, -- Elton Carvalho -- Gromacs Users mailing list * Please search the archive at http://ww

Re: [gmx-users] Problem with running crystal simulation

Is your topology correctly connecting the atoms through the box wall so you have a periodic molecule? Have you set "periodic_molecules = yes" in your MDP files? Cheers, -- Elton Carvalho On Mon, Nov 23, 2015 at 3:58 PM, Ben Tam wrote: > Dear GROMACS user, > I have a problem here

Re: [gmx-users] Lennard-Jones potential not matching with published data

GROAMCS defines sigma as the distance where the LJ potential is zero. Some forcefields define sigma as the bottom of the well. Checking wether your reference uses 6-12 or 6-9 LJ funcions may also help. Cheers! -- Elton Carvalho Departamento de Física Universidade Federal do Paraná -- Gromacs Users

[gmx-users] Gromacs performance on virtual servers

datacenter (their plan is to decentralize the colocation), so network latency may be higher than the traditional setup, which may affect scaling. Does this argument make sense or am I missing something on cloud management 101? Cheers. -- Elton Carvalho Departamento de Física Universidade Federal do

Re: [gmx-users] Lennard-Jones potential not matching with published data

On Thu, Jul 24, 2014 at 10:47 PM, Justin Lemkul wrote: > > On 7/24/14, 4:30 PM, Elton Carvalho wrote: >> >> I've been there before. >> >> Check which Lennard-Jones function was used to publish the data to >> which you are comparing. There are some no

Re: [gmx-users] Gromacs-4.6.6 + openmpi 1.6: no output running in 2 nodes

n MPI and the behavior is the same. Thanks in advance! -- Elton Carvalho -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un

Re: [gmx-users] Gromacs-4.6.6 + openmpi 1.6: no output running in 2 nodes

to stdout/stderr. When I run mdrun -v, there's nothing in the stderr or stdout of the job, even though that mpi hello-world successfully writes to stdout. For this reason I don't believe it's a filesystem issue. Any other ideas? I'm puzzled. Thanks! [1] http://mpitutorial.com/mpi

Re: [gmx-users] gromacs 4.6.4 version - nvt equilibration error

ch the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or

[gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

r or added the different terms? Thanks in advance, -- Elton Carvalho -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

ov 14, 2016 at 8:04 PM, Elton Carvalho wrote: > Hello, fellow Gromacs Users, > > I'm trying to model P3DDT with CGenFF according to the instructions at > paramchem.org, running the cgenff_charmm2gmx.py script as provided in > their website. All this is being done on gromacs 2016

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

erwise it would have seemed like it had to be a > code bug. > > Maybe we could add a warning for including the same file twice? Does > anybody do that deliberately E.g with different preprocessor variables > defined? > > Mark > > On Tue, 15 Nov 2016 00:30 Elton Carvalho w

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

kes sense. Otherwise it would have seemed like it had to be a >> > code bug. >> > >> > Maybe we could add a warning for including the same file twice? Does >> > anybody do that deliberately E.g with different preprocessor variables >> > defined? >

Re: [gmx-users] Problem with running crystal simulation

, that's a symptom of bad topology. If it doesn't blow up > in > > NVT and does in NPT, check your pressure options in the MDP: "pcoupl", > > "pcoupltype", "tau_p", "ref_p" and "compressibility". > > > > Is yo

Re: [gmx-users] NPT compress Box using negative Pressure

hat you are trying to accomplish. Greetings from a cloudy yet hot Natal, -- Elton Carvalho -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support

Re: [gmx-users] mdrun error

osting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Elton Carvalho -- Gromacs Us

Re: [gmx-users] Fwd: removing some atoms

Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search

Re: [gmx-users] Distance between atom A and the nearest image of atom B

rchive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >

Re: [gmx-users] Why GROMACS is generating so many output trajectory files?

st? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Elton Carvalho -- Gromacs Users mailing list * Please search the arc

Re: [gmx-users] cut the trajectory in small sub-trajectories

On Mon, Jan 18, 2016 at 7:43 AM, Cuong Nguyen wrote: > [...] I want to get the average temperature as a function of > the box's length. Do you have any suggestions? > Hello, Cuong, You can convert your trajectory to the .gro format using trjconv then write a program/script that uses the velociti

Re: [gmx-users] *.pdb file for the Tip4p/ice model

_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.o

Re: [gmx-users] Gromacs 2018 installation failed

mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/

Re: [gmx-users] Gromacs 2018 installation failed

Liao wrote: > Hello Elton, > > Thanks a lot for your information, I already sent an e-mail to the > administrator, > hopefully they will fix it. > > > All the best, > Qinghua > > > On 02/09/2018 08:03 PM, Elton Carvalho wrote: > >> Hello, Qinghua, &

[gmx-users] By what tool is the atomptypes.atp file used?

rs form a sunny and warm (as usual) Natal, Elton References: [1] http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field [2] http://manual.gromacs.org/documentation/current/user-guide/file-formats.html -- Elton Carvalho -- Gromacs Users mailing list * Please search the a

[gmx-users] Nonsense timing accounting with OpenCL in Haswell

GPU has >25% more load than the CPU. This imbalance wastes CPU resources. Core t (s) Wall t (s)(%) Time:12080.732 1510.092 800.0 (ns/day)(hour/ns) Performance:2.861 8.389 [ LOG FILE ENDS ] Cheers from an unbearably

Re: [gmx-users] Nonsense timing accounting with OpenCL in Haswell

; printing to see whether you notice a few abnormal timings or whether all > are nonsensical. > > Roland > > > From: Elton Carvalho mailto:elto...@gmail.com>> > Date: Thu, 24 Jan 2019 at 04:06 > Subject: [gmx-users] Nonsense timing accounting with OpenCL in Hasw

Re: [gmx-users] error while running gmx grompp

> > > __ > > Dinesh Nath, Ph.D. > > The University of Oklahoma > > Postdoctoral Research Fellow > > Department of Chemistry & Biochemistry > > Institute for Natural Products Applications > > & Research Technolog

Re: [gmx-users] Fwd: gmx trjcat

t;> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >>