Re: [gmx-users] Gromacs 2018 and GPU PME

-ntomp 6 -npme 1 -gputasks 0001 I am seriously confused here. Also, the number of ranks is 8, while the number of threads is 6? Is -ntomp now specifying the _per-rank_ number of threads, i.e. the actual number of threads for this job would be 48? Thank you, Alex On 2/9/2018 8:25 AM

Re: [gmx-users] GPU load from nvidia-smi

to a 50% boost from -pme gpu. A colleague just walked in and I shared the bottom of that md.log. Expletives of awe and admiration were loudly exchanged. We're doing the upgrade for my 8-year old desktop-turned-linux-box with a single puny GTX 960 -- just because it would be dumb not to. Hats off to you

Re: [gmx-users] GPU load from nvidia-smi

tem -- is this no longer a correct assumption? Thanks, Alex On Thu, Feb 8, 2018 at 12:44 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Yes. Note the new use of -gputasks. And perhaps check out > http://manual.gromacs.org/documentation/2018-latest/ > user-guide/mdrun-performance

Re: [gmx-users] GPU load from nvidia-smi

heck out > http://manual.gromacs.org/documentation/2018-latest/ > user-guide/mdrun-performance.html#types-of-gpu-tasks > because > things are now different. > > gmx mdrun -ntmpi 3 -npme 1 -nb gpu -pme gpu is more like what you want. > > Mark > > On Thu, Feb 8, 2018 at 8:36

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

With -pme gpu, I am reporting 383.032 ns/day vs 270 ns/day with the 2016.4 version. I _did not_ mistype. The system is close to a cubic box of water with some ions. Incredible. Alex On Thu, Feb 8, 2018 at 12:27 PM, Szilárd Páll <pall.szil...@gmail.com> wrote: > Note that the act

[gmx-users] GPU load from nvidia-smi

reports 65% load on 0 and nothing on 1 and 2. Is this normal? Thanks, Alex -- 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)subscribe

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

. That in itself might be publishable... 3. I will run tests on a system, for which I know the performance with 2016.4 so we can compare, especially with -pme gpu Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

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

Got it. Given all the messing around, I am rebuilding GMX and if make check results are the same, will install. We have an angry postdoc here demanding tools. Thank you gentlemen. Alex On Thu, Feb 8, 2018 at 10:50 AM, Szilárd Páll <pall.szil...@gmail.com> wrote: > On Thu, Feb 8, 201

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

Are you suggesting that i should accept these results and install the 2018 version? Thanks, Alex On Thu, Feb 8, 2018 at 10:43 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > PATH doesn't matter, only what ldd thinks matters. > > I have opened https://redmi

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

That is quite weird. We found that I have PATH values pointing to the old gmx installation while running these tests. Do you think that could cause issues? Alex On Thu, Feb 8, 2018 at 10:36 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Great. The manual run to

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

uh, no sir. > 9/39 Test #9: GpuUtilsUnitTests ***Timeout 30.43 sec On Thu, Feb 8, 2018 at 10:25 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Those all succeeded. Does make check now also succeed? > > Mark > > On Thu, Feb 8

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

rd Páll <pall.szil...@gmail.com> wrote: > It might help to know which of the unit test(s) in that group stall? Can > you run it manually (bin/gpu_utils-test) and report back the standard > output? > > > -- > Szilárd > > On Thu, Feb 8, 2018 at 3:56 PM, Alex <nedoma

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

Here's some additional info: # # cat /proc/driver/nvidia/version NVRM version: NVIDIA UNIX x86_64 Kernel Module 390.12 Wed Dec 20 07:19:16 PST 2017 GCC version: gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.6)

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

Forwarding colleague's email below, any suggestions highly appreciated. Thanks! Alex *** I ran the minimal tests suggested in the cuda installation guide. (bandwidthTest, deviceQuery) and then I individually ran 10 of the samples provided. However, many of the samples require a graphics

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

I did hear yesterday that CUDA's own tests passed, but will update on that in more detail as soon as people start showing up -- it's 8 am right now... :) Thanks Mark, Alex On 2/8/2018 7:59 AM, Mark Abraham wrote: Hi, OK, but not clear to me if followed the other advice - cleaned out all

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

Nope, still persists after reboot and no other jobs running:  9/39 Test  #9: GpuUtilsUnitTests ***Timeout  30.59 sec Any additional suggestions? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

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

I am rebooting the box and kicking out all the jobs until we figure this out. Thanks! Alex On 2/8/2018 7:27 AM, Szilárd Páll wrote: BTW, timeouts can be caused by contention from stupid number of ranks/tMPI threads hammering a single GPU (especially with 2 threads/core with HT), but I'm

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

Mark, Peter -- thanks. Your comments make sense. -- 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)subscribe requests visit

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

postdoc's work... All of those were with -nb cpu though. Could those factors have affected our regression tests? 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

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

-nophys.dir/all] Error 2 CMakeFiles/Makefile2:971: recipe for target 'CMakeFiles/check.dir/rule' failed make[1]: *** [CMakeFiles/check.dir/rule] Error 2 Makefile:546: recipe for target 'check' failed make: *** [check] Error 2 Any ideas? I can post the complete log, if needed. Thank you, Alex

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

Hi Mark, Nothing has been installed yet, so the commands were issued from /build/bin and so I am not sure about the output of that mdrun-test (let me know what exact command could make it more informative). Thank you, Alex *** > ./gmx -version GROMACS version:    2018 Precis

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

And this is with: > gcc --version > gcc (Ubuntu 5.4.0-6ubuntu1~16.04.6) 5.4.0 20160609 On Tue, Feb 6, 2018 at 1:18 PM, Alex <nedoma...@gmail.com> wrote: > Hi all, > > I've just built the latest version and regression tests are running. Here > is one error: > > &qu

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

g to worry about? Thank you, Alex -- 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)subscribe requests visit https://maillist.sys.kth.

Re: [gmx-users] GMX 2018 and CUDA 9.1

That is not what I meant. PME on GPU was related to my interest in the latest GMX version. The interest in the newest CUDA version is coming from another group member, so I am just making sure things are compatible. Thanks! Alex On 2/6/2018 12:17 AM, Mark Abraham wrote: Hi, Yes

[gmx-users] GMX 2018 and CUDA 9.1

Hi all, We're about to update our software, which includes CUDA libs. Before we do, has the latest Gromacs version been tested with CUDA 9.1? Because I really want that PME offloaded to GPU! :) Thank you, Alex -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] generating movie file

No, there are other tools for that (e.g. pymol + avidemux). I too was wondering if trjconv could produce an mp4 and add Morgan Freeman's voice as narration to my glorious trajectory, but was disappointed. Very useful for supplemental files for journals with IF>10. Maybe gmx developers should

[gmx-users] (no subject)

Dear users and developers! I have a question about replica exchange sampling and simulation annealing method. Well, I have a protein (TubulinG) X-ray, however it lack last 10-11 residues, which are probably exposured to the solvent (and it seems are flexible enough to be invisible for X-ray). The

Re: [gmx-users] (no subject)

A beginner in what? Your question has nothing to do with Gromacs. Alex On 1/20/2018 11:12 PM, Sankaran SV . wrote: Dear all, I am a beginer. I would like to know the purpose of adding ions during the simulation process. -- Gromacs Users mailing list * Please search

Re: [gmx-users] potential profile with PBC

Okay, ignore my question. :) I really should have looked at the description of how gmx potential does its job. Switching to -correct fixes the issue, even if this is somewhat fake. Alex On Wed, Jan 17, 2018 at 3:49 PM, Alex <nedoma...@gmail.com> wrote: > Hi all, > > I have a

[gmx-users] potential profile with PBC

are different at the boundaries. There are no external fields in the system, nothing like that. When choosing the group for the potential calculations, i select System. This potential difference seems fundamentally wrong, given PBC. Any suggestions? Thanks, Alex -- Gromacs Users mailing list * Please

Re: [gmx-users] VMD Compatibility Question

surfaces and their interactions with other things especially at the nanoscale cannot be accurately described by classical MD. It's a topic far beyond the scope of this board. Alex On 12/28/2017 11:55 PM, Ethan Hsiao wrote: Users Charlie and I want to perform MD simulations on transition metal

Re: [gmx-users] Grompp error : Incorrect number of parameters

ular term (first term in U-B with two constants) from elsewhere and you want to use it in the U-B format, it is an absolutely trivial task. All you have to do is set the U-B distance-dependent energy component to zero. Alex On 12/20/2017 12:05 AM, RAHUL SURESH wrote: Hi Thank you Mark. On W

Re: [gmx-users] WHAM

need. Three months is actually a reasonable amount of time to get the basics of MD and Gromacs right. Without those basics, it is completely pointless to try doing any work. Alex On Mon, Dec 18, 2017 at 8:57 AM, rose rahmani <rose.rhm...@gmail.com> wrote: Dear Justin,I don't hav

Re: [gmx-users] WHAM

of what it is not. Good luck! Alex On 12/17/2017 1:44 PM, Justin Lemkul wrote: On 12/17/17 3:39 PM, Rose wrote: Why you don't answer me?is there anything wrong in my question? Contrary to popular opinion, I don't know everything :) If I don't reply to a question, it is because I have nothing

Re: [gmx-users] Gromacs 2018b1: Computing PME on GPUs

Sorry, I am unable to respond to your question, but could you please comment on performance difference with and without PME on GPU? Thanks, Alex On 12/10/2017 10:28 PM, Jernej Zidar wrote: Hi, I’ve been testing the first beta of the upcoming Gromacs 2018, where one of the main features

Re: [gmx-users] umbrella sampling

ugh. Cheers, Alex On Sun, Nov 26, 2017 at 23:10 rose rahmani <rose.rhm...@gmail.com> wrote: > Hi; > > This is md_pull.mdp > > integrator = md > dt = 0.001 > nsteps = 200 > nstxout = 0 > ns

Re: [gmx-users] Applying an electric field on lipids

So, you have a charged protein under a high electric field, moving and bumping into an unrestrained lipid bilayer. Maybe use position restraints, those are well documented in the Gromacs manual. Alex On 11/20/2017 11:23 PM, Sithara Perera wrote: The .mdp file parameter for electric field

Re: [gmx-users] Applying an electric field on lipids

this mean that it's something like "E-z = 1 -0.0007 0.0 " in your mdp file? The units are V/nm, not mV/nm. Alex On Mon, Nov 20, 2017 at 6:15 PM, Sithara Perera < sithara.perera1...@gmail.com> wrote: > Yes. The system was stable and simulations showed that the b

Re: [gmx-users] Applying an electric field on lipids

Do you precede your production simulation with a relaxation run without an electric field? Alex On 11/20/2017 12:16 PM, Sithara Perera wrote: Dear gmx-users, I'm doing molecular dynamic simulations of protein interaction with lipid bi layers using CGmartini force fields under an electric

Re: [gmx-users] virtual site, dummy massive site

And the things that affect the motion of the things with LJ interactions. :) Alex On 11/18/2017 3:49 PM, Mark Abraham wrote: Hi, Only things with LJ interactions can influence the LJ energy. Mark On Fri, 17 Nov 2017 21:06 Faezeh Pousaneh <fpoosa...@gmail.com> wrote: I have 2 que

Re: [gmx-users] salt concentration

ow you calculated the critical box size depending on the the concentration. On Tue, Nov 14, 2017 at 9:12 AM, Alex <nedoma...@gmail.com> wrote: It makes no difference whether you use -np/-nn or -conc. Your box is simply too small to result in a nonzero ion count with something like 0.002

Re: [gmx-users] salt concentration

any number of ions in there, but back-calculate the corresponding concentration, given the box volume, and you'll see that it's not what you want. This is exactly what GMX does when you call -conc. Alex On 11/13/2017 11:54 PM, Netaly Khazanov wrote: Thanks for your prompt replay. I thougnt

Re: [gmx-users] walls and E-z

acs implementation of walls. My setup is incredibly simple, as I am trying to polarize an ionic solution along the Z-axis. Alex On 11/9/2017 3:16 PM, Alex wrote: Got it --  filed on redmine. With a "real" wall and E-z = 0.1V/nm, only five ions cross, which can be confirmed by simple

Re: [gmx-users] walls and E-z

Got it -- filed on redmine. With a "real" wall and E-z = 0.1V/nm, only five ions cross, which can be confirmed by simple calculations as sufficient to counteract the external field, given the membrane's own crossing barrier. Alex On Thu, Nov 9, 2017 at 2:21 PM, Dan Gil <dan.gil9

Re: [gmx-users] walls and E-z

is impermeable? Alex On Thu, Nov 9, 2017 at 12:03 AM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 08/11/17 22:29, Alex wrote: > >> Okay, same thing with 0.5V/nm. I think it's fairly safe to say that >> there's >> something wrong here... >> > Hav

Re: [gmx-users] walls and E-z

Okay, same thing with 0.5V/nm. I think it's fairly safe to say that there's something wrong here... Alex On Wed, Nov 8, 2017 at 12:25 PM, Alex <nedoma...@gmail.com> wrote: > Good question. Dielectric breakdown of water is generally poorly > understood and the threshold depends

Re: [gmx-users] walls and E-z

as a reviewer. :) That aside, I believe your suggestion is sound, at least to see if what I observe is an outright bug. Thanks, Alex On Wed, Nov 8, 2017 at 10:39 AM, Dan Gil <dan.gil9...@gmail.com> wrote: > Yes I saw your plot and it is simply around 0 with walls. > > What is the

Re: [gmx-users] walls and E-z

is that of a system without any driving field. The electric field is already quite high (0.1 V/nm) and of course I could go completely nuts and exceed the experimental dielectric breakdown threshold values for water, but the question remains, no? Thanks, Alex On 11/8/2017 9:58 AM, Dan Gil

[gmx-users] walls and E-z

= 1.0 rvdw= 1.0 vdwtype = cut-off cutoff-scheme = Verlet Any ideas? Thanks, Alex -- 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

Re: [gmx-users] Lost particles while sorting

ng seems to be okay in my simulation. :) Well, except for... That combination is one of the very large number of things in GROMACS that I know very little about. But a new topic might get the interest of any who do know! ... for this combination. I will post as soon as I can confirm this weirdn

Re: [gmx-users] Lost particles while sorting

. ;) Thanks, Alex On 11/2/2017 6:11 PM, Mark Abraham wrote: Hi, Yes that seems consistent with some theories Berk had when we chatted over lunch. Specifically, if the linear potential is too weak then you wouldn't get the repulsion you seek. Clearly you've found some other more basic ways that a system

Re: [gmx-users] Lost particles while sorting

Will upload to dropbox later (strict 'no external cloud' institutional policy). I don't know if the tpr is completely self-contained, so please let me know if you need the ff folder as well. Thank you, Alex On Wed, Nov 1, 2017 at 4:42 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote:

[gmx-users] Lost particles while sorting

= 3dc fourierspacing = 0.135 rcoulomb= 1.0 rvdw= 1.0 vdwtype = cut-off cutoff-scheme = Verlet This uses a custom type "opls_996" properly defined in ffnonbonded of the FF (custom OPLSAA). Any suggestions? I can provide more info, if neede

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

it was never intended. :) Best of luck! Alex On Wed, Oct 18, 2017 at 3:14 PM, Rose <rose.rhm...@gmail.com> wrote: > Oh,you mean that i should make My sheet then just optimize it(with out > putting charge) and then convert it to .pdb file and use it in MD as an > input? I have checked

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

structure is "suitable" in principle, as long as the interactions are set properly. It is hard to give any advice beyond that. Simulation of "custom" structures is a lot of effort. If your system of interest is small, an alternative to all of this could be DFTMD simulations using CP2K

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

ive us an idea of what you're trying to do? Alex On 10/18/2017 1:09 PM, rose rahmani wrote: Hi I am a beginner user of GROMACS, i want to simulate the interaction of nano sheet with amino acid ,but i dont know what should do, how should i behave with these structures ? is there any tutoroial f

Re: [gmx-users] How to perform simulation of carbon nanotube in GROMACS in NPT ensemble?

I just replied to Neha's post. You are having issues that have nothing to do with Gromacs, i.e. Gromacs is simply responding to incorrect system setup. Please generate a proper periodic topology and use a PBC-compatible box. Alex On 10/8/2017 3:47 PM, Ming Tang wrote: Dear list, I have

Re: [gmx-users] Equilibration using position restraints in NPT

In addition, the CNT edges have to be periodically commensurate. On 10/8/2017 3:36 PM, Alex wrote: PBC for crystals are not set this way, this is why the simulator is turning the CNT into a pogo stick. Prior to any simulations, please calculate the correct PBC-compatible axial length using

Re: [gmx-users] Equilibration using position restraints in NPT

, then proceed with EM, etc. Alex On 10/8/2017 3:29 PM, Neha Gandhi wrote: Thank you Mark. The nanotube is 2x2x13 nm long. Then I use editconf with -c and -d 2 and solvate using spc216.gro. How can I calculate box size after NVT so that I get density of 1 or 0.99 when using pressure coupling

[gmx-users] lower-end GPUs

in this case. Any suggestions on what to invest in for the sub-$500 range per card? Thank you, Alex -- 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

Re: [gmx-users] Regarding box length variation after npt and production md run

Box size fluctuations during NPT are normal, while their degree may or may not be. In any case, your questions at the moment aren't about Gromacs. They suggest that you need to get a better idea on what barostats are, what they do, how they work, etc, etc. Alex On 9/24/2017 10:46 PM, Dilip

Re: [gmx-users] GPU-accelerated EM

. Before my initial post, we already decided on CPU-only EM and your advice to move the EM portion elsewhere (e.g. our old machines) is even better. Thanks, Alex On Fri, Sep 8, 2017 at 4:27 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > The em log files report

[gmx-users] GPU-accelerated EM

, Alex -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo

[gmx-users] GPU-accelerated performance

PUs. Any suggestions on further increase what we can squeeze out of this thing for a single simulation? The relevant mdp section is below (CHARMM defaults, really). What would you try in your mdrun line? Thanks! Alex cutoff-scheme   = Verlet nstlist

[gmx-users] FEP: mdp setting for mutation

Hi, Following changes are made in the mdp file for mutation analysis.Can anyone tell me is there anything wrong here? ; init_lambda_state0123456789 10 11 12 13 14 15 16 17 18 19 20 vdw_lambdas = 0.00 0.05 0.10 0.15

Re: [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation

Thank you very much, It worked with NVT, but the water molecule is not going though the channel at 0.01 nm per ns but It worked when i increased the pull_coord1_rate to 0.5 nm per ns from 0.01nm per ns but could not get proper histogram and energy profile. What parameters i need to change in

Re: [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation

The error is actually telling you exactly what is wrong. First relax your system with pressure coupling, then do pull in NVT. Or, possibly adjust the system in such a way that 'direction' pull could be used instead of 'direction-periodic'. Alex On 8/20/2017 1:53 AM, Alex Mathew wrote

Re: [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation

Dear Justin, As per the manual i have changed parameters as tcoupl = berendsen tc_grps = Protein Non-Protein Chain_B tau_t = 1.01.01.0 ref_t = 310 310 310 ; pcoupl = berendsen pcoupltype

[gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation

Dear all, In order to obtain the PMF diagram of a water molecule through membrane protein channel, I set up a simulation system and try to run with pull_coord1_geometry= direction-periodic. To correct te error following changes are made in the mdp file {error (Can not have dynamic box while

Re: [gmx-users] dielectric constant 4

A meaningful answer to your question is incredibly non-trivial. Also, you will need a reference for your epsilon value. "Someone on gmx-users told me, because I don't feel like doing my own research" may not look very good in a manuscript. Alex On 8/16/2017 5:14 PM, Mohammad Zahid

[gmx-users] positioning molecule at desired location

Dear all, I want to keep a water molecule at a particular position of a protein channel. I need to pull this across the channel and observe the energy diagram by PMF. can anyone tell me how I can keep water molecules at a particular position. thank you. -- Gromacs Users mailing list * Please

Re: [gmx-users] Difference in omega angles!!

by turning the entire triplet (or a quadruplet) into a solid structure? Also, congrats on professorship! :) Alex -- 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.o

Re: [gmx-users] (no subject)

at a very low temperature. Say, 5-10K? This is prior to solvating, etc. I've never worked with MnO2, so I just can't say anything more specific, sorry. I hope this helps. Alex On Wed, Aug 9, 2017 at 12:10 PM, gangotri dey <holyriv...@gmail.com> wrote: > Dear Alex and Mark, > > Thank yo

Re: [gmx-users] (no subject)

nd points 1-4 aren't something your doctoral advisor already mentioned, maybe you should find another advisor. Alex Hi, Are you trying to implement a model that you know is capable of produce a surface that does not deform in unexpected ways? Mark On Mon, 7 Aug 2017 16:35 gangotri dey <ho

[gmx-users] x2top and default dihedral type

it to '3' by default in OPLS, since all dihedrals are of type 3 in that forcefield. At any rate, i get 1 and want 3. Any help? Thanks, Alex -- 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

Re: [gmx-users] CHARMM36 for GMX

compliment. As always, thanks. Alex On Wed, Aug 2, 2017 at 12:59 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/2/17 2:52 PM, Alex wrote: > >> Yeah, those are indeed there for the particular molecules, thanks. I >> understand that this is the only way to go, it's j

Re: [gmx-users] CHARMM36 for GMX

with that catalog you mentioned. Like, place a carboxyl termination somewhere, or have a hole in a bulk sheet of graphene, etc. In any case, thank you. Alex On Wed, Aug 2, 2017 at 12:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/2/17 2:38 PM, Alex wrote: > >> Huh.

[gmx-users] CHARMM36 for GMX

ffnonbonded.itp has pretty much all default charges set to zero. Is this called for?? I apologize in advance if this is a dumb or misdirected question, as I've never worked with CHARMM before. Thank you, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] pulling of a molecule through protein-membrane system

Dear Justin, Well, Charmm-gui not providing an option to make a long box in one direction. So is it fine increasing the box and adding the water in Charmm-gui output pdb file and proceed? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] pulling of a molecule through protein-membrane system

Dear all gromacs users, I would like to build a protein-membrane system to perform umbrella simulation; I need to calculate the molecule transportation by pulling it from top to bottom. In the tutorial, it says "Some force fields include everything you need. For instance, it is unwise to try to

Re: [gmx-users] Molecular Simulation using Ionic liquid

You can't just assume that your favourite tool is the one for the job. Mark That just stung me right through the heart. :) Alex -- 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

Re: [gmx-users] Damping for pulled group

have my own MD simulator, which features all of that stuff, but Gromacs runs many, many, MANY times faster. :) Alex -- 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

Re: [gmx-users] Damping for pulled group

I mean would it be hard to add a damping term. Sorry, half asleep. :) Alex On Tue, Jul 18, 2017 at 2:44 PM, Alex <nedoma...@gmail.com> wrote: > Hi all, > > This is more of a question about where I should make a suggestion for the > developers. It turns out that Gromacs pull

[gmx-users] Damping for pulled group

, Alex -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo

Re: [gmx-users] NPT problem

. Until you make some effort to learn about graphene and crystals (prior to solvating and doing other things), nothing will work and noone here will be able to help. Alex On Fri, Jul 14, 2017 at 1:09 AM, <mohammad.r0...@yahoo.com> wrote: > The graphene is 9*9 nm, and I proposed the box to

Re: [gmx-users] NPT problem

or pbc to work the box in your case has to be a certain size corresponding to the graphene dimensions. And no, it is not simply its approximate X-Y dimensions. Alex ---- *From:* Alex <nedoma...@gmail.com> *To:* Discu

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

eally more of a general comment, because more and more people are trying to simulate solid-state structures with Gromacs. Best of luck! Alex On 7/13/2017 6:43 PM, Jason Zhu wrote: Dear Alex, Many thanks for your replies and helping. I totally agree with your comments about infinite

Re: [gmx-users] mdrun -rerun

unsurprisingly, mdrun refuses to -rerun on multiple cores in this case, only -nt 1 works. Thanks! Alex On Thu, Jul 13, 2017 at 3:35 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Right, sorry. You always had the index group, and I forgot you had to > declar

Re: [gmx-users] mdrun -rerun

throws this: "ERROR 1 [file prod_rerun.mdp]: Energy group exclusions are not (yet) implemented for the Verlet scheme" But the original simulation was performed with Verlet cutoff scheme. Do I change that regardless of this fact? Thanks, Alex On Thu, Jul 13, 2017 at 3:10 PM, Ma

Re: [gmx-users] mdrun -rerun

Same error in v. 2016.1. On Thu, Jul 13, 2017 at 2:39 PM, Alex <nedoma...@gmail.com> wrote: > Here you are, as run on the production tpr: > > $ gmx make_ndx -f prod.tpr > GROMACS:gmx make_ndx, VERSION 5.0.5 > > > > > Reading structure file

Re: [gmx-users] mdrun -rerun

, Jul 13, 2017 at 2:35 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > What does gmx make_ndx think? > > Mark > > On Thu, Jul 13, 2017 at 10:34 PM Alex <nedoma...@gmail.com> wrote: > > > Hi Mark, > > That's the problem: the names are exactly as they

Re: [gmx-users] mdrun -rerun

can make them with gmx make_ndx, gmx select, > or your favourite text editor, and feed them to gmx grompp -n. You normally > get spoiled with automatically generated groups that happen to match > moleculetypes and such. So probably you have SOL already. > > Mark > > On Thu, Jul 13, 20

[gmx-users] mdrun -rerun

the interactions in the following group pairs: DEC-DEC BUT-BUT CBD-CBD DEC-BUT DEC-CBD When setting energygrp-excl with the following pairs, I immediately get a grompp error saying that DEC isn't an energy group. Since I've never done this before, can you please share your wisdom? Thank you, Alex

Re: [gmx-users] NPT problem

, say, equal to m, then multiply the dihedral parameters by that number. And do NOT use bond constraints -- you are simulating a crystal. Alex On Thu, Jul 13, 2017 at 10:45 AM, <mohammad.r0...@yahoo.com> wrote: > Hi All GROMACS users, > > > > I created graphene with na

Re: [gmx-users] NPT problem

h, do you understand what that CNT tutorial is doing, or are you blindly following it? This stuff requires effort. Noone can help otherwise. Alex On Thu, Jul 13, 2017 at 10:45 AM, <mohammad.r0...@yahoo.com> wrote: > Hi All GROMACS users, > > > > I created graphene with nano

Re: [gmx-users] problem: gromacs run on gpu

Can you try to open the script in vi, delete the mdrun line and then manually retype it? On 7/12/2017 11:03 PM, leila karami wrote: Dear Gromacs users, I am doing md simulation on Gromacs 5.1.3. on GPU in Rocks cluster system using command: gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

lved by setting a larger nrexcl value. In your case, you solved it with turning off intramolecular coupling. In fact, if you set your nrexcl to something like 4 or 5, you may not even need to turn off the coupling. But then again, I don't know where the parameters came from. Alex -- Gromacs User

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

are the nonbonded types for boron and nitrogen? 3. How was the topology obtained? If x2top was used, was the BN sample in a box with in-plane PBC? Alex On 7/11/2017 8:39 PM, Jason Zhu wrote: Hello Gromacs Community, I am trying to calculate the solvation free energy of a hBN sheet following Justin

Re: [gmx-users] output pdb reformatted

different simulations) everything seemed okay. Thanks! Alex On Tue, Jul 11, 2017 at 2:40 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/11/17 4:01 PM, Alex wrote: > >> Hi all, >> >> I have a tiny acetonitrile molecule here. The input pdb prior to EM is &

[gmx-users] output pdb reformatted

topology input. Thank you, Alex -- 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)subscribe requests visit https://maillist.sys.kth.se

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