[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/lis

[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

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] Fat-bottom restrain

s 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? Reg

Re: [gmx-users] Fat-bottom restrain

Flat-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 tot

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

ing smart-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. > > C

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, &

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

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] 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 other

[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.s

[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] 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

[gmx-users] Frozen group moves!

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

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] 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

[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] 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

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

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) Thanks Al

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

20 CUDA runtime: 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://maillis

[gmx-users] gmx gangle in a for loop

roup $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/Sup

[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 at

[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

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

v 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 of A

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

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

, 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

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

[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/Suppor

[gmx-users] Annealing

0 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 ht

[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

[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] 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 of a

[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

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] 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] Thin film drifting

fting 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 > &g

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

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. 15:16,

[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-

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 Auto

[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 * P

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

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

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 forc

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

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

l it 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 htt

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

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

[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:

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

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 > > O

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

onsider 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] 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 be

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

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 sm

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

[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

[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

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

depositing 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

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

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! *

[gmx-users] naming of CH2 groups in pdb file

named DEP of a molecule in the input file was mapped to an entry in the topology database, but the atom CH2 used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Regards, Alex -- Gromacs Users mailing list

[gmx-users] Gromacs mdrun for k20 and cpu

command), Thank you very much. Yours sincerely 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] Polymer not diffusing into membrane

lone to equilibrate it. 2. Take the final box size of the lipid bilayer and use it to place the Polymer at specific point just above the lipid bilayer. 3. Perform energy minimization on the system4. Perform NVT and NPT5. Run the simulation Any advice woul

Re: [gmx-users] Polymer not diffusing into membrane

lation? Are you sure it is long enough to see what you > want to see? > On 12 Aug 2014 07:15, "Alex s" wrote: > > > Dear Gromacs users > > I'm not sure if this a question suitable for this forum but I would > > greatly appreciate it if you can help me in

Re: [gmx-users] Polymer not diffusing into membrane

y any movement of the polymer along the Z axis, its seems that there's something 'repelling' it any time it gets close to the bilayer. I've attached a text version of my mdp file, I would like to attach snapshots of my system setup but it would exceed the 50 KB limit. Thanks

Re: [gmx-users] Polymer not diffusing into membrane

where I have to manually edit water boxes and position them to fill the empty space in the system box. ThanksAlex > Date: Wed, 13 Aug 2014 10:21:42 -0400 > From: jalem...@vt.edu > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Polymer not diffusing into membrane > > >

Re: [gmx-users] Polymer not diffusing into membrane

I obtained all of my forcefield, coordinate and topology files from the MARTINI website. > Date: Wed, 13 Aug 2014 11:29:52 -0400 > From: jalem...@vt.edu > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Polymer not diffusing into membrane > > > > On 8/13/14, 10:45

[gmx-users] Segmentation fault mdrun

he time step from to 0.04 to 0.03. >From what I'm describing, does it seem as if the fault lies with the system >set up? or the mdp file? or could it be a compiler issue? What information >should I be looking for in my output file to perhaps determine wh

Re: [gmx-users] Segmentation fault mdrun

oking for in point 3? Thanks Alex > Date: Sun, 31 Aug 2014 13:20:31 -0400 > From: jalem...@vt.edu > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Segmentation fault mdrun > > > > On 8/31/14, 1:17 PM, Alex s wrote: > > Hi > > I'd really appreciate

Re: [gmx-users] Segmentation fault mdrun

ystem so a time step of 0.04 shouldn't be a problem. Regarding the link you've given, points 1 and 4 are not applicable to my situation, I've tried point 2 and found issues. What should I be looking for in point 3? Thanks Alex > Date: Sun, 31 Aug 2014 13:20:31 -0400 > From: ja

Re: [gmx-users] Segmentation fault mdrun

systems, I have found that 2 of the systems which experienced segmentation fault had a warning that the pressure scaling was more than 1 % . However the other systems that experienced segmentation fault presented no such warning yet the force imbalance was as high as 6 %. Could this be the issu

[gmx-users] gmx cluster

gromos -cl out.pdb -g out.log is it okay? 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 requests visit

[gmx-users] permeation events- ion channels in bilayer

/ nanotubes/files/permeation.tcl Unfortunately all the time it gives zero value (I have tried for different upperEnd and lowerEnd ), but i can visualize the water movements in VMD screen. Kindly provide your valuable suggestions, since i don't have much expertise in coding/programming. Alex -- Gr

[gmx-users] including .itp file to system

Hello everyone, i wanted to perform a Protein-Ligand Simulation,i created .itp,psf,.par etc files for ligand and am able to make topol.top and conf.gro or the protein using pdb2gmx .Forcefield is CHARMM27 Now i im confused how to include ligand into my system.as per tutorial we are provided with .g

[gmx-users] Regarding .itp file to the system

Justin, Thanks for your quick reply so how i should proceed with .itp file as per your tutorial .gro file is required ,if i add "new.itp" to topol.top there might be problem that atom number mismatch between the conf.gro which produced for protein alone When i tried to load mol2 file in charmmgui

[gmx-users] Regarding .itp file to the system

Dear Justin, Thanks for your previous answer i quoted below "1. Process the protein with pdb2gmx and obtain a .top and coordinate file in whatever format you like. 2. Generate a ligand topology, #include its .itp file in the .top 3. Append the ligand coordinates to those of the protein from step

[gmx-users] Forcefiled

Dear all, When we select a United atom ff and When we select All atom forcefield,is it depends on the number of amino residues? what difference it will make in either cases (looking for any link or source where i can find the details ) and regarding the selection of any force filed i have seen in

[gmx-users] Protein Ligand simulation

such as hydrophobic pi-pi etc Is is possible to do any competitive inhibition study using gromacs? kindly share some useful articles best Alex!! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] Protein Ligand simulation

such as hydrophobic pi-pi etc Is is possible to do any competitive inhibition study using gromacs? kindly share some useful articles best Alex!! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[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

[gmx-users] ion channel in lipid bilayer

Hi all! I have a question concerning immersion of the ion channel (four subunits with extracellular domains and a bundles of helixes) into the lipid bilayer. 6 years ago I used some tutorial or mailing lists, which described the way from KALP15 tutor. With CCR5 model there were no problems at all

[gmx-users] Fwd: ion channel in lipid bilayer

I'm sorry for repeat, but nobody answered the question and I decided to duplicate the request. Maybe it is a problem with a form of question or its content, please, point me the mistake. Hi all! I have a question concerning immersion of the ion channel (four subunits with extracellular domains an

Re: [gmx-users] ion channel in lipid bilayer

Dear Peter, thank You for responce! I've already prepared toplogy file, here is a content: '''' ; Include forcefield parameters #include "charmm36-jul2017.ff/forcefield.itp" #include "/home/dikov/alex/WORK/lipid/charmm36.itp" #include &q

[gmx-users] Fixing dssp images using m2p file

Dear Gromacs experts, Which option i need to use to correct the dssp image as given in the link. (i have to get full part upto 100 ns in the box) You can see the right side is not full in the box, i marked in the black box https://drive.google.com/file/d/1QkpFOLvOcrSyv1U6HkRorYrKgKxGCskS/view?

[gmx-users] tilt angle between the axis of a protein normal to the membrane

Dear gromacs users, I would like to calculates the tilt angle between the axis of a protein (its a nanotube, embedded perpendicular to the lipids-along z) and the normal to the membrane . I have used gmx gangle -f XXX.xtc -s XX.tpr -g1 vector -g2 z -oav angle.xvg, is it correct approach? -- Gr

[gmx-users] pull distance vs direction?

Hi to all, Is there any theoretical difference between pull_coord1_geometry= distance pull_coord1_geometry= direction (distance vs direction) other than simple distance pulling and pulling in specific direction.? I used to pull "distance" for a water molecule to transport through the cyc

[gmx-users] (no subject)

Dear all, How to modify a mdp file to generate two different tpr files, from the same initital coordinates of a Na 1.5 voltage gated channel in the membrane (it is already relaxed and in a closed state)? I need to set parameters for the system with a voltage of -80 mV and than, after 100 ns start i

[gmx-users] Electric field or CompEl protocol?

Dear all, Which protocol, Electric field section or the CompEl, I should use in the situtation: 1. I built an ion channel by homology, prepared a bilayer membrane, embeded my protein and run a simulation to relax the system (100 ns) 2. my channel was closed all the time. 3. I want to run four para

Re: [gmx-users] Electric field or CompEl protocol?

Dear Alex! Yes, I thought about all Your reflections and I'm also not sure that CompEl is well parameterzied for a non-specialist like me and the electric field is more intuitive for me. However, when I saw the dimension 'V/nm' for the first time, I thought that something mus

[gmx-users] Electric field or CompEl protocol?

rinciple, it is a solid idea, but I think this algorithm is clunky and how it agrees with PBC is unclear to me. If you get clean and reasonable data, please let everyone know! :) Alex On 5/20/2018 1:16 AM, alex rayevsky wrote: >* Dear Alex! *>>* Yes, I thought about all Your reflectio

[gmx-users] secondary structure element constraining

Dear users! Did anybody meet the problem of positional constraints applied to the secondary structure, namely keeping the 310-helix stable all the time? I've modelled the substructure - a bundle of alpha helices with a 310 helix segment (longer, thinner, reactive) on the one of them. And I need to

[gmx-users] secondary structure element constraining

degree of oscilation) less appropriate methods? or simple genrestr with 1 kJ forces ? Thank You! On 6/10/18 3:04 AM, alex rayevsky wrote: >* Dear users! *>>* Did anybody meet the problem of positional constraints applied to the *>* secondary structure, namely keeping the 310-heli

[gmx-users] secondary structure element constraining

Yes, it does... Should I follow this advices http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints ? Phi/Psi lines are like in the sample, with only changed values of atom indexes and angles, measured with pymol of gromacs tools ai ajakal | type | label | phi |

[gmx-users] Cys-Cys bonding

Dear Users and masters! I know that gromacs can prepare the topology with covalent bonding of cys-cys bridges in the individual chain on fly. However, when two different chains are connected with such bonds and the intital geometry is satisfactory (distance, angle) It doesn't work. It was done wit

[gmx-users] Heavy metals parameterisation

the same. 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/ma

Re: [gmx-users] Heavy metals parameterisation

Thanks Justin, I am looking for the effect of heavy metals in channel proteins. Could you please provide me some links or paper to where i can start QMMM. Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posti

Re: [gmx-users] Heavy metals parameterisation

Dear Justin, More specifically, I'm looking for the transport properties of proteins in presence and absence of heavy metals- how heavy metals affecting the transportation of molecules across the channels. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Suppor

Re: [gmx-users] Heavy metals parameterisation

I'm looking something like this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2856166/ Here the mercury bind to Cys residue and inhibiting the channel. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can

Re: [gmx-users] Heavy metals parameterisation

Thanks, In general for parameterising the small molecules or heavy metals VMD- FFTK is sufficient? or is there any other tools I need to use other than the Gaussian package (for DFT or MP2). -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_List

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