[gmx-users] Negative part of the reaction coordinate in PMF

of the negative part are and are not considered. The -sym yes flag doesn't help as the two end points of the RC don't overlap each other. 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

Re: [gmx-users] Lincs warning and Bond length not finite

on graphene are properly pre-equilibrated. Alex On 5/3/2020 6:39 PM, Mohamed Abdelaal wrote: Hello everyone, I am simulating the evaporation of non protein molecules on a graphene sheet. I am using gromos force field and hence the lincs constrain are set to all-bonds. I have done the energy

[gmx-users] conformation tensor

he end-to-end distance but not the end-to-end vector. I wonder if there is a gmx tool to either directly calculate to conformation tensor or the end-to-end vector to extract the x and y directions of that vector later on? Thank you Alex -- Gromacs Users mailing list * Please search the archive at

[gmx-users] wham - Bootstraping

. Updated rapid wham stuff. (evaluating only 395 of 24250 contributions) Updated rapid wham stuff. (evaluating only 1854 of 24250 contributions) Would you please let me know how 395, 1854 ... are being considered for evaluation? and what do they mean? Regards, Alex -- Gromacs Users mailing list

Re: [gmx-users] GROMACS performance issues on POWER9/V100 node

unable to productively bug our sysadmins (the cluster is institution-wide and there are only two people who have to deal with all the users). I myself do not have admin privileges on this machine. The only reason I commented was that Jon revitalized my old thread. ;) Alex On 4/24/2020 2:31 PM

Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com

Hi Magnus, I see, many thanks for the insights. On Thu, Apr 23, 2020 at 2:45 AM Magnus Lundborg < magnus.lundb...@scilifelab.se> wrote: > Hi Alex, > > pull-group1-pbcatom lets you specify the exact atom used as the PBC > reference. Both 0 and -1 are special cases. For

Re: [gmx-users] GROMACS performance issues on POWER9/V100 node

. At this point, if someone could figure out a clear set of build instructions in combination with slurm/mdrun inputs, it would be very much appreciated. Alex On 4/23/2020 9:37 PM, Kevin Boyd wrote: I'm not entirely sure how thread-pinning plays with slurm allocations on partial nodes. I always reserve

Re: [gmx-users] Spec'ing for new machines (again!)

Hi Szilárd, We haven't decided yet on what price point& performance level we would be settling on, but this is overall great advice, thanks a lot. Alex On 4/21/2020 4:32 PM, Szilárd Páll wrote: Hi, Note that the new generation Ryzen2-based CPUs perform even better than those we benchma

Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com

d consider it as one of the pulling groups instead of the large group? Thank you Alex On Mon, Apr 20, 2020 at 8:46 AM Magnus Lundborg < magnus.lundb...@scilifelab.se> wrote: > Hi Alex, > > I don't see why it would need pull-group1-pbcatom = -1. Why not pick a > central atom? > >

Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com

. Regards, Alex On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg < magnus.lundb...@scilifelab.se> wrote: > Sorry, about the statement about pbcatom -1. I was thinking about 0. I > don't know if pbcatom -1 is good or not in this case. > > Regards, > > Magnus > > On 202

Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com

Any comment on this would be so appreciated! Regards, Alex On Sat, Apr 18, 2020 at 2:12 PM Alex wrote: > Dear all, > To generate the initial configurations for umbrella sampling, I conducted > a simple pulling simulation by which a single-small molecule (mol_A) is > being dragged a

[gmx-users] Artifact in pull-pbc-ref-prev-step-com

of gro file in which change from one from to another is the distance between the COM of the thin-film and mol_A? 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

Re: [gmx-users] Spec'ing for new machines (again!)

outlines a path towards upgrading our existing nodes. Thanks Kevin, this is very informative. Alex On 4/17/2020 8:52 PM, Kevin Boyd wrote: Yes, that's it. I think consumer-class Nvidia cards are still the best value, unless you have other applications that need the benefits of industrial cards

Re: [gmx-users] Spec'ing for new machines (again!)

additional speed boost if we also used AMD GPUs. Nope, haven't seen the paper, but quite interested in checking it out. Is this the latest version? https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.26011 Thank you, Alex On 4/17/2020 6:29 PM, Kevin Boyd wrote: Hi, AMD CPUs work fine

[gmx-users] Spec'ing for new machines (again!)

work with NVIDIA cards? Will we have to install AMD GPUs? Does current Gromacs perform well on AMD-based rigs? 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

Re: [gmx-users] dt in mdp

On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote: > > > On 4/10/20 9:16 AM, Alex wrote: > > Thank you for the response. > > > > > > On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: > > > >> > >> On 4/10/20 8:13 AM, Alex wrote

Re: [gmx-users] dt in mdp

Thank you for the response. On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: > > > On 4/10/20 8:13 AM, Alex wrote: > > Dear Justin, > > Any comment please? > > Sorry, haven't had power/network for a while due to some bad storms here. > > GROMOS force fie

Re: [gmx-users] dt in mdp

Dear Justin, Any comment please? Regards, Alex On Tue, Apr 7, 2020 at 5:38 PM Alex wrote: > Thanks Justin for the response. > Please find below the mdp file. > The system is a thin film made out of a epoxy molecule, picture in be > below link, with water on top and bottom of the

Re: [gmx-users] dt in mdp

= Thin_fiml SOL %- Thank you Alex On Tue, Apr 7, 2020 at 5:06 PM Justin Lemkul wrote: > > > On 4/7/20 5:00 PM, Alex wrote: > > Dear all, > > After minimization and equalizations using nvt (v-rescale) and npt (both > > berendsen and ;Parrinello-Ra

[gmx-users] dt in mdp

the simulation wouldn't run well for 200 ns. But I expect that it also crashes for example around 6 ns as the with the dt = 0.002 the simulation last only 3 ns. Any comment that helps to understand the problem would be highly appreciated. Regards, Alex -- Gromacs Users mailing list * Please

Re: [gmx-users] Issue with PMF

Thanks Justin for the response. On Thu, Apr 2, 2020 at 3:21 PM Justin Lemkul wrote: > > > On 4/2/20 12:53 PM, Alex wrote: > > Dear all, > > By using the below setting I am getting a very nice umbrella histogram > and > > iact also shows a very good integrated

[gmx-users] Issue with PMF

0 reference position column: No Found 2501 times in prd_pullf.1.xvg %-- Thank you, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users

Re: [gmx-users] Thin film drifting

On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel wrote: > Den 2020-03-29 kl. 19:43, skrev Alex: > > Thanks. > > > > On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel < > sp...@xray.bmc.uu.se> > > wrote: > > > >> Den 2020-03-29 kl.

Re: [gmx-users] Thin film drifting

Thanks. On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel wrote: > Den 2020-03-29 kl. 15:16, skrev Alex: > > Thank Prof. van der Spoel for the response. > > No, it isn't. The thin film is solid. There are interaction within the > thin > > film and with water in the i

Re: [gmx-users] Thin film drifting

significantly in the production along both x and y directions. Best regards, Alex On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel wrote: > Den 2020-03-29 kl. 05:24, skrev Alex: > > Dear all, > > In a system, I have a thin_film (infinitive in x-y directions) with water > &

[gmx-users] Thin film drifting

However the thin film drift specially in x and y directions whereas I was expecting to have no drifting for the thin film, If I understood correctly the usage of the comm-grps! Would you please let me know how I can stop drifting of the thin film? Thank you, Alex -- Gromacs Users mailing list

Re: [gmx-users] comm-grps

on removal group (VCM groups). However, the two following options work: “comm-grps = thin_film Mol_A SOL” or “comm-grps = Other SOL” Where the Other group contains the thin film and molecule A, the pull_group2 and pull_group1, respectively. Which one do you recommend, please? Thank you Alex On M

[gmx-users] comm-grps

system my question is that if I am allowed to use: "comm-grps = thin film" and also "comm-mode = Linear-acceleration-correction" ? Thank you Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before pos

[gmx-users] Fwd: Reproducibility of a PMF plot

Any comment, please? Thank you, Alex -- Forwarded message - From: Alex Date: Sun, Mar 15, 2020 at 8:16 PM Subject: Reproducibility of a PMF plot To: Dear all, Of course it is always good to prove that a MD simulation is reproducible by repeating several replicas

[gmx-users] Reproducibility of a PMF plot

using umbrella sampling in which the bootstrap analysis is performed to calculate the standard deviation? Or for an alchemical free energy calculation where the e.g. the block averaging is used? Regards, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

[gmx-users] gmx traj

(which I am obviously happy to increase)? 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

[gmx-users] Annealing

ps So, according to above, I am confused if the simulation would start from A or B pointed out above? I like it to start from B, and considering the CPT file, but later I don't want to append in mdrun. Thank you Alex -- Gromacs Users mailing list * Please search the archive at http://www.g

[gmx-users] How to add osmotic stress

How to introduce osmotic stress on a simulation system to study the transportation differences in varying conditions.( protein-membrane system) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] gmx genconf

nput could be -trj.xtc, but no trajectory as output has been mentioned there apparently. Regards, 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/Mai

Re: [gmx-users] Center of mass motion removal

ist and unfortunately the whole droplet moves around: https://drive.google.com/open?id=1_aVJzfXJQWQ-aP_rHwgEXGeas7KWcnuo BTW, I used a proper .tpr file where the molecule are all intact. Thank you Alex On Fri, Dec 13, 2019 at 7:50 PM Justin Lemkul wrote: > > > On 12/13/19 10:51 AM, Alex wrote

Re: [gmx-users] Center of mass motion removal

, by removing those as well, nothing would remain. Regards, Alex On Thu, Dec 12, 2019 at 6:09 PM Alex wrote: > Dear Justin, > As you recommended I invoked the trjconv -pbc cluster and trjconv -center > separatedly, and also, I used a proper reference .gro file (where > everything is in

Re: [gmx-users] Center of mass motion removal

that the droplet stay in center of droplet even if one or two molecules leave the droplet? Thank you Alex On Sat, Dec 7, 2019 at 6:31 PM Justin Lemkul wrote: > > > On 12/6/19 4:37 PM, Alex wrote: > > Thanks Justin, > > > > As I said, I have already used the "trj

Re: [gmx-users] Center of mass motion removal

conv to have the COM of the droplet fixed at a single point for all frames of the trajectory? Regards, Alex On Fri, Dec 6, 2019 at 8:45 AM Justin Lemkul wrote: > > > On 12/5/19 3:47 PM, Alex wrote: > > Hi all, > > > > I have a droplet containing two molecules types o

[gmx-users] Center of mass motion removal

of mass motion of the whole trajectory? I have already applied the gmx trjconv -pbc mol Then gmx trjconv -pbc cluster -center yes However, as I knew, they can not stop the COM motion. Thank you Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] droplet

Dear all, The surface area (calculated by gmx sasa) of a droplet of a molecule, reduces during temperature quenching, I wonder if anybody has an idea to explain that by calculation a meaningful quantity of the droplet? Thank you Alex -- Gromacs Users mailing list * Please search the archive

[gmx-users] gmx gangle in a for loop

$i and name C10 plus group $i and name C20' -g2 vector -group2 'cog of group 0 plus cog of group $i' -n ind.ndx -f ind.xtc -s ind.tpr -oav aver$i.xvg -oh hist$i.xvg done Thank you Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/G

[gmx-users] Works well on CPU, not on GPU

: 8.0 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/mailman

Re: [gmx-users] Fwd: gmx trjcat

Hi Paul, I though you mean converting the .gro files to .xtc file using *trjcat *(which was my initial question), sorry about that. I see now, I just used *trjconv* to convert gro file them to .xtc files and then ... . .gro trjconv> .xtc --trjcat> .xtc(or trr) Thank

Re: [gmx-users] Fwd: gmx trjcat

Hi, Paul, I guess you understood the question wrongly. I have some *.gro files and I want to concatenate them to have a trr (or xtc) trajectory. Justin, Yes indeed, It would be great if gmx trjcat could concatenate the gro files. Regards, Alex On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul

[gmx-users] Fwd: gmx trjcat

Any comment on this, please? Thanks -- Forwarded message - From: Alex Date: Sat, Oct 26, 2019 at 9:38 AM Subject: gmx trjcat To: Dear all, I want to concatenate some gro file to have a trr or xtc trajectory file out of them as gro files are also acceptable as input files

[gmx-users] gmx trjcat

t *gro* g96 pdb tng So, I fed the .gro files in as input files likes; gmx trjcat -f c*.gro -o trajout.trr However, I get below error that; Fatal error: gmx trjcat can only handle binary trajectory formats (trr, xtc, tng) Any comment is highly appreciated. Regards, Alex -- Gromacs Users mailin

[gmx-users] supercell

Dear all, I have a gromacs trajectory for which I need to generate supercell of its last 5ns. The supercell needs to be two times larger than the initial cell from each side. I wonder if there is a tools available in gromacs for doing that? Regards, Alex -- Gromacs Users mailing list * Please

Re: [gmx-users] Frozen group moves!

Hi, Thanks for the response. On Tue, Oct 22, 2019 at 02:04 David van der Spoel wrote: > Den 2019-10-21 kl. 21:24, skrev Alex: > > Dear all, > > I freeze a group in my system in all directions as normal: > > freezegrps = GR > > freezedim

[gmx-users] Frozen group moves!

be the reason and how one can avoid that to happen? Regards, 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

[gmx-users] simulating glass materials using GROMACS

Dear experts, I would like to simulate NASICON type glass using GROMACS. The paper I referred to here used LAMPP (https://pubs.acs.org/doi/abs/10.1021/jp5094349). How should I proceed for this kind of study with GROMACS? What kind of forcefield I can use in GROMACS? can anyone provide a starting

[gmx-users] cpt file

Hi all, Is it possible to truncate the check point file ( *.cpt) similar to the trajectory using for instance gmx trjconv -e? Regards, 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

[gmx-users] Fwd: cut in gmx clustsize

Any comments, please? Thanks, Alex -- Forwarded message - From: Alex Date: Fri, Oct 4, 2019 at 13:58 Subject: cut in gmx clustsize To: Dear all, In clustering what is usually defined as a criteria is a cut-off so that if two atoms or molecules are closer to each other less

[gmx-users] cut in gmx clustsize

the molecule? Regards, 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/mai

Re: [gmx-users] index.ndx file of all cluster

Any comment is highly appreciated. Regards, Alex On Sun, Sep 22, 2019 at 3:34 PM Alex wrote: > Dear all, > The gmx clustsize -mcn maxclust.ndx gives the index.ndx file only for the > largest cluster formed in the system, I wonder if it is possible to have > the index.ndx for ot

[gmx-users] index.ndx file of all cluster

and then the second-largest cluster would be the new largest one and so on ... . Regards, 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] Fat-bottom restrain

somewhere should I mention that I have used (I haven't used) flat-bottom restrains in these simulation? Thank you Alex On Wed, Sep 11, 2019 at 8:01 PM Mark Abraham wrote: > Hi, > > It's certainly conceivable that such restraints are ineffective in some run > modes. However, "on

Re: [gmx-users] Fat-bottom restrain

art-bottom restraints instead? I haven't hear the smart-bottom one, would you please explain more? or address me to a reference? > > Jokes aside, why does it matter if your molecules move into the next > periodic image? Just to avoid percolation across the period box. > > Cheers, > Bil

Re: [gmx-users] Fat-bottom restrain

Hi, Any comment, please? Thank you. Alex On Mon, Sep 9, 2019 at 10:22 PM Alex wrote: > Hi Mark, > > Thank you for your response. > Here are the part of options that gmx energy gives me out: > > 9 Coulomb-(SR)10 Coul.-recip. > 1

Re: [gmx-users] Fat-bottom restrain

-bottom posres energy would remain absolutely zero! I rechecked everything and I don't see any problem with the way I have set the flat-bottom restrain. Any comment would be highly appreciated. Thank you, Alex On Sat, Sep 7, 2019 at 10:47 AM Mark Abraham wrote: > Hi, > > The total potenti

[gmx-users] Fat-bottom restrain

are also out of the smaller box in several replica's simulations each with 100 ns. The only reason I can imagine is that the K=4184 KJ/(mol. nm^2 is probably too low to keep the molecules inside the smaller box! I wonder if you know any other potential reason? how can I find out the reason? Regards, Alex

Re: [gmx-users] Performance, gpu

nm out -s out.tpr -g out.log -v -dlb yes -gcom 1 -nb gpu -npme 44 -ntomp 4 -ntomp_pme 6 -tunepme yes would you please help me choose a correct combinations of -npme and ... to get a better performance, according to the attached case.log file in my previous email? Regards, Alex On Sat, Aug 24, 2019 at 1

[gmx-users] Performance, gpu

-myQ5rP85UWKb1262QDPa6kYhuzHPzLu 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

[gmx-users] Switching CPU to GPU in a simulation

, 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] Gromacs FEP tutorial

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html > -- 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

[gmx-users] Gromacs FEP tutorial

Can anyone tell me which thermodynamics cycle was used in the tutorial? for FEP. -- 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

[gmx-users] Trajectory

s too. So, I wonder if there is any way to save me from re-simulating? I already have the .trr file which contains all the atoms during the whole simulation but it has collected the data in a very low frequency respect to the xtc. Regards, Alex -- Gromacs Users mailing list * Please search

Re: [gmx-users] Xeon Gold + RTX 5000

Perfect, thanks a lot! We are less constrained by cost, so we'll go straight to 2080Ti. You guys already saved us a few grand here. ;) Alex On 7/17/2019 7:34 PM, Moir, Michael (MMoir) wrote: Alex, The motherboard I am using with the 9900K is the ASUS WS Z390 PRO. The PRO version has

Re: [gmx-users] Xeon Gold + RTX 5000

Gentlemen, thank you both! Michael, would you be able to suggest a specific motherboard that removes the bottleneck? We aren't really limited by price in this case and would prefer to get every bit of benefit out of the processing components, if possible. Thanks, Alex On 7/17/2019 10:44

Re: [gmx-users] Keep having to path gromacs when opening a new terminal

cd /etc/profile.d sudo ln -s /usr/local/gromacs/bin/GMXRC GMXRC.sh On 7/16/2019 8:14 PM, Israel Estrada wrote: Hello Users, I've compiled GROMACS successfully on my machine, but the gmx_mpi command is not recognized until I enter the command source /usr/local/gromacs/bin/GMXRC everything

Re: [gmx-users] Xeon Gold + RTX 5000

That is excellent information, thank you. None of us have dealt with AMD CPUs in a while, so would the combination of a Ryzen 3900X and two Quadro 2080 Ti be a good choice? Again, thanks! Alex On 7/16/2019 8:41 AM, Szilárd Páll wrote: Hi Alex, On Mon, Jul 15, 2019 at 8:53 PM Alex wrote

[gmx-users] Xeon Gold + RTX 5000

with more than 50K particles. Could you please comment on whether this is a cost-efficient and reasonably powerful setup? Your past suggestions have been invaluable for us. Thank you, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

[gmx-users] force constant (K_fb)

(Kj mol-1 nm-2) for k_fb with no reason and it works fine in my case, do you think I should check if any other smaller k_fb works and use the smaller one? Regards, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Check point file

the xtc and trr files to have all at 80 ns. Regards, Alex On Mon, Jun 24, 2019 at 5:41 AM Mark Abraham wrote: > Hi, > > On Mon., 24 Jun. 2019, 11:21 Alex, wrote: > > > Thanks Mark. > > With not be able to append to the simulation files, you mean, I should > not

Re: [gmx-users] Check point file

the trjcat/eneconv used for later concatenation know that the new outputs should be assigned to the time t = 8000*1*? In the other case, if I use the -cpi state.cpt in the gmx mdrun, everything are being continued from t = 10. Thank you. Alex On Mon, Jun 24, 2019 at 1:55 AM Mark Abraham wr

Re: [gmx-users] Amber force field for metal Surface

is, it may or may not be appropriate to use Gromacs for this purpose, but it needs to be a judicious, carefully researched choice. Alex On 6/24/2019 12:50 AM, Kumari Shilpa wrote: I am calculating interaction energy between a polymer molecule (75 atoms) and an iron surface. For polymer I

Re: [gmx-users] Fwd: (-13.000000 Total charge should normally be an integer), Facing problem while running gromacs

It is not an error message, but a note. If grompp quits with an error, please read it carefully. Alex On 6/23/2019 11:27 PM, kalpana wrote: Kindly help to understand this error message becz with previous installation with same setting files, there was no error. The error message is as follows

[gmx-users] Check point file

to have the case.80ns.cpt unlike the case.80ns.xtc and trr. So, I wonder if it is meaningful if I use the case.100ns.cpt,, case.80ns.xtc and case.80ns.trr to continue from 80 ns point? Thank you. Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] oplsaa tooology for urea

es_for_MDS For the life of me, I can't find any rtp entries related to urea in oplsaa.ff, which is my FF of choice. Justin, any thoughts? 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

Re: [gmx-users] Parrinello-Rahman vs. Nose-Hoover

permanently from all simulators forever -- except for maybe incredibly well-behaved pre-relaxed ensembles larger than 100K atoms. Alex On 5/28/2019 9:08 PM, Anh Vo wrote: Hi, Previously, as my colleague performed the same simulation with me (POPC bilayer membrane under equibiaxial tension

Re: [gmx-users] gmx trjconv

Dear all, Any comment on this, please? Thank you. Alexander On Thu, May 23, 2019 at 10:02 AM Alex wrote: > Dear GMX user, > I have a 110 GB trajectory from which I would like to extract only the > trajectory of the part of my interest, the rest is water. To do so, I use &

Re: [gmx-users] non-water solvent + gmx solvate

Hi Kevin, Emailed to your address. Just to clarify, there is really only one issue, which is that we have a particular input that is making us stick with 2018. Once that's been figured out, I'll be able to enjoy the great new functionality in solvate. ;) Thanks, Alex On 5/27/2019 8:15 PM

Re: [gmx-users] non-water solvent + gmx solvate

/msg37181.html), but Szilard assured me that it wasn't much of an issue. Indeed, the build worked fine with our "usual" simulations. This one experiencing issues (minor with 2018 and catastrophic with 2019) is new and it this setup isn't expected to go away. Thanks a lot. Alex On 5

Re: [gmx-users] non-water solvent + gmx solvate

Hi Kevin, I'm using 2018.2 -- had to roll 2019 back because it segfaults on a certain simulation setup (I posted earlier about that, got no responses). Kind of a disappointing situation... I guess I will use packmol or just script it with insert-molecules. Alex On 5/26/2019 8:31 AM, Kevin

[gmx-users] non-water solvent + gmx solvate

idn't like what I found (http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation). I wonder if anything has changed... 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?

[gmx-users] gmx trjconv

Dear GMX user, I have a 110 GB trajectory from which I would like to extract only the trajectory of the part of my interest, the rest is water. To do so, I use " echo 1 | mpiexec_mpt -n 1 gmx_mpi trjconv -f tot.xtc -s topol.tpr -o nonwater.skip4.xtc -skip 4". The extracting goes very slow

Re: [gmx-users] External electric field applied to water box

Oops. Yes, we most certainly have a semiisotropic setup. I think I misread the original message. Well, this is why I don't post much lately. :-) Alex On Wed, May 22, 2019, 11:39 AM Justin Lemkul wrote: > > > On 5/22/19 1:34 PM, Alex wrote: > > To quickly chime in: we routinely

Re: [gmx-users] External electric field applied to water box

. I suspect issues with setup in your case. Alex On 5/22/2019 11:17 AM, Justin Lemkul wrote: On 5/22/19 9:03 AM, Nidhin Thomas wrote: Dear Justin, Thanks a lot for the prompt reply. I ran another simulation with a larger box size with and without external electric field (field direction

Re: [gmx-users] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)

Yup, your assessment agrees with our guess. Our HPC guru will be taking his findings, along with your quote, to the admins. Thank you, Alex On Thu, May 9, 2019 at 2:51 PM Szilárd Páll wrote: > On Thu, May 9, 2019 at 10:01 PM Alex wrote: > > > Okay, we're positively unable to r

Re: [gmx-users] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)

Okay, we're positively unable to run a Gromacs (2019.1) test on Power9. The test procedure is simple, using slurm: 1. Request an interactive session: > srun -N 1 -n 20 --pty --partition=debug --time=1:00:00 --gres=gpu:1 bash 2. Load CUDA library: module load cuda 3. Run test batch. This starts

Re: [gmx-users] 2019.2 build warnings

. Alex On 5/2/2019 12:42 AM, Alex wrote: Hi Szilárd, Thanks a bunch. I have upgraded to 2019.2 and a fairly large "production" test seems to be running without any issues. Alex On 5/1/2019 5:07 AM, Szilárd Páll wrote: Hi, You can safely ignore the errors as these are caused by

Re: [gmx-users] 2019.2 build warnings

Hi Szilárd, Thanks a bunch. I have upgraded to 2019.2 and a fairly large "production" test seems to be running without any issues. Alex On 5/1/2019 5:07 AM, Szilárd Páll wrote: Hi, You can safely ignore the errors as these are caused by properties of your hardware that the te

Re: [gmx-users] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)

Well, unless something important has changed within a year, I distinctly remember being advised here not to offload anything to GPU for EM. Not that we ever needed to, to be honest... In any case, we appear to be dealing with build issues here. Alex On 5/1/2019 5:09 PM, Kevin Boyd wrote: Hi

Re: [gmx-users] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)

gt; On Wed, May 1, 2019 at 5:56 PM Alex wrote: > > > Well, my experience so far has been with the EM, because the rest of the > > script (with all the dynamic things) needed that to finish. And it > > "finished" by hitting the wall. However, your comment does touch upon

[gmx-users] Flory-Huggins parameter

Dear all, Does anybody know how to calculate the Flory-Huggins parameter? The engine for all atoms MD simulations is Gromacs and the system of interest is an emulsion of epoxy resin and surfactant in water. Thank you. Best regards, Alexander -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)

out to see if things make a difference for the better. I am less confident about setting strides because it is unclear what the job manager provides in terms of the available core numbers. I will play around some more and report here. Thanks! Alex On Wed, May 1, 2019 at 3:49 PM Mark Abraham wr

[gmx-users] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)

stions on building and running GMX on Power9? 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 vis

Re: [gmx-users] 2019.2 build warnings

Oh, cool -- thanks! I guess we will be replacing the older builds, then. Funny enough, you may not recall it, but the hardware for particular box was purchased with your own advice, which served us very well up until now. :) Again, thank you. Alex On 5/1/2019 5:07 AM, Szilárd Páll wrote

Re: [gmx-users] 2019.2 build warnings

.tar.gz?dl=0 If you can help us figure this out, it will be great! Thanks, Alex On 4/29/2019 4:25 AM, Szilárd Páll wrote: Hi, I assume you used -DREGRESSIONTEST_DOWNLOAD=ON case in which the tests are downloaded and unpacked under BUILD_TREE/tests/regressiontests-release-2019-[SUFFIX

Re: [gmx-users] 2019.2 build warnings

a tarball, but not sure it's all that necessary. I don't remember which tests failed, unfortunately... Thank you! Alex On 4/25/2019 2:54 AM, Szilárd Páll wrote: Hi Alex, On Wed, Apr 24, 2019 at 9:59 PM Alex wrote: Hi Szilárd, We are using neither Ubuntu 18.04, nor glibc 2.27, but the problem

Re: [gmx-users] 2019.2 build warnings

Hi Szilárd, We are using neither Ubuntu 18.04, nor glibc 2.27, but the problem is most certainly there. Until the issue is solved one way or another, we will be staying with 2018.1, i guess. $ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description:    Ubuntu

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