Re: [gmx-users] seeming paradox with gmx wham

You actually pointed this symmetry situation out when I was calculating something that's already been submitted, so the gratitude is all mine. Hopefully, it doesn't produce much of a difference in that particular case, but I really should have listened. The path to correcting possible artifacts is

Re: [gmx-users] seeming paradox with gmx wham

On 3/12/18 6:59 PM, Alex wrote: Great, thanks. I believe this necessitates an acknowledgment. You go by J. A. Lemkul in your papers, correct? That would work. Much obliged :) -Justin On Mon, Mar 12, 2018 at 4:56 PM, Justin Lemkul wrote: r On 3/12/18 6:54 PM, Alex

Re: [gmx-users] seeming paradox with gmx wham

Great, thanks. I believe this necessitates an acknowledgment. You go by J. A. Lemkul in your papers, correct? On Mon, Mar 12, 2018 at 4:56 PM, Justin Lemkul wrote: > r > > On 3/12/18 6:54 PM, Alex wrote: > >> Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point,

Re: [gmx-users] seeming paradox with gmx wham

r On 3/12/18 6:54 PM, Alex wrote: Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's still a small system. My sampling pull code is below, I only modified the bare minimum to work with the new pull code syntax and to enable spherical slices (radius varying from near-zero

Re: [gmx-users] seeming paradox with gmx wham

Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's still a small system. My sampling pull code is below, I only modified the bare minimum to work with the new pull code syntax and to enable spherical slices (radius varying from near-zero to 1.5 nm): pull =

Re: [gmx-users] Regarding minimum size

Hi, That's not a valid way to use these components. Whatever you're trying to do shouldn't be attempted by trying to call mdrunner.mainFunction() twice. Mark On Mon, Mar 12, 2018 at 9:54 PM Chhavi Yadav wrote: > I wrote this code and was running the debugger: > > > int

Re: [gmx-users] nve simulation

Hi, The list can't accept attachments. There's a plot in the reference manual that shows some indicative minimal drifts, which would be a good place to search. :-) Mark On Mon, Mar 12, 2018 at 9:31 PM Jo wrote: > Hello, > > I would like to run an NVE simulation but am

Re: [gmx-users] Regarding minimum size

On 3/12/18 4:52 PM, Chhavi Yadav wrote: I wrote this code and was running the debugger: int main(int argc, char *argv[]) { int rc; MD mdrunner; rc = mdrunner.mainFunction(argc, argv); printf("Potential Energy from integrator: %.6f\n", mdrunner.epot); mdrunner.epot

Re: [gmx-users] seeming paradox with gmx wham

On 3/12/18 3:42 PM, Alex wrote: I actually understood your tutorial perfectly well. What I didn't expect is such a significant dependence on direction (assuming spherical symmetry clears the situation). I also had to use direction-periodic instead of distance in your tutorial, because the

Re: [gmx-users] Regarding minimum size

I wrote this code and was running the debugger: int main(int argc, char *argv[]) { int rc; MD mdrunner; rc = mdrunner.mainFunction(argc, argv); printf("Potential Energy from integrator: %.6f\n", mdrunner.epot); mdrunner.epot = 0; t_state *t =

[gmx-users] nve simulation

Hello, I would like to run an NVE simulation but am having trouble conserving the energy. From some past postings on the email list, I understand that some neighborlist buffer parameters need to be adjusted, however I still am not able to conserve energy. I am simulating a box of 1000 SPCE

Re: [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

Dear Mark, Thanks for your response. Yes, I have gone through that document. (link: http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf). I have tried using energy-group pairs to take from table file and those are not in the energygrps should take from Gromacs. But the document says that

Re: [gmx-users] seeming paradox with gmx wham

Sorry, i meant 4 nm tall, not wide. On 3/12/2018 1:42 PM, Alex wrote: I actually understood your tutorial perfectly well. What I didn't expect is such a significant dependence on direction (assuming spherical symmetry clears the situation). I also had to use direction-periodic instead of

Re: [gmx-users] seeming paradox with gmx wham

I actually understood your tutorial perfectly well. What I didn't expect is such a significant dependence on direction (assuming spherical symmetry clears the situation). I also had to use direction-periodic instead of distance in your tutorial, because the box is 4 nm wide and grompp is

Re: [gmx-users] seeming paradox with gmx wham

On 3/12/18 3:28 PM, Alex wrote: Thanks! Just to make sure I'm doing this right this time. By merely changing the dim directive with everything else following your tutorial, I would be probing the spherical domain around the pore with a bunch of different radius values? Because this is

Re: [gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex

On 3/12/18 3:26 PM, SHYANTANI MAITI wrote: Dear all, I have been simulating a protein-protein complex using gromacs for 100ns. after the completion of job, I find that the rmsd values have undergone a sudden increase after 20ns of the simulation. Is my simulation going wrong somewhere? Can

Re: [gmx-users] seeming paradox with gmx wham

Thanks! Just to make sure I'm doing this right this time. By merely changing the dim directive with everything else following your tutorial, I would be probing the spherical domain around the pore with a bunch of different radius values? Because this is exactly what I want. Thanks, Alex

[gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex

Dear all, I have been simulating a protein-protein complex using gromacs for 100ns. after the completion of job, I find that the rmsd values have undergone a sudden increase after 20ns of the simulation. Is my simulation going wrong somewhere? Can protein-protein complexes be simulated in gromacs?

Re: [gmx-users] Regarding minimum size

On 3/12/18 2:05 PM, Srinivasa Ramisetti wrote: I think the minimum coordinates are (0,0,0) Not really. GROMACS will accept negative coordinates and then re-wrap them into the periodic box with its origin at (0,0,0). An actual error message and full command from the OP would be helpful

Re: [gmx-users] Regarding minimum size

I think the minimum coordinates are (0,0,0) Srinivasa On 12/03/2018 18:01, Chhavi Yadav wrote: Hi Justin, Thanks for the reply. I meant this : In our application, we need to randomly sample coordinates for atoms. When we were doing that, we got an error message for one of the random coordinate

Re: [gmx-users] Regarding minimum size

Hi Justin, Thanks for the reply. I meant this : In our application, we need to randomly sample coordinates for atoms. When we were doing that, we got an error message for one of the random coordinate samples because the sample coordinate was smaller than the minimum coordinates. What is this

Re: [gmx-users] Regarding minimum size

On 3/12/18 1:30 PM, Chhavi Yadav wrote: Hello, This is regarding the minimum size or resolution used in gromacs for sampling coordinates of atoms. I know that the maximum size is the matrix box. Can someone please let me know what the minimum is? I'm not sure if this is the answer to your

Re: [gmx-users] Help with interpreting message for fatal error

Hi Gregory, It's periodically connected and I am applying adaptive biasing/pulling (forgot to say). If you have special experience with that kind of setup, I'd be interested in hearing it. Otherwise, it's quite standard, and yes, parmbsc1. -- Viveca On Mon, Mar 12, 2018 at 6:53 PM, Gregory

Re: [gmx-users] Help with interpreting message for fatal error

On 3/12/18 1:40 PM, Viveca Lindahl wrote: Hi Justin, I'm using semi-isotropic pressure coupling and the periodicity is along z. I should say that I'm also adaptively biasing a base pair to open, which is triggering the fluctuations. I guess you mean using only OpenMP? I have not tried that

Re: [gmx-users] Help with interpreting message for fatal error

Hi Justin, I'm using semi-isotropic pressure coupling and the periodicity is along z. I should say that I'm also adaptively biasing a base pair to open, which is triggering the fluctuations. I guess you mean using only OpenMP? I have not tried that no, thanks for the suggestion. Now I changed to

Re: [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?

Hi, On Mon, Mar 12, 2018 at 4:19 PM Douwe Pollmann wrote: > Dear Gromacs users, > > I am currently working on a coarse-grained model where I want to fix atoms > (Cb's) on a certain distance from Ca-Ca bonds, so that they can rotate > freely. This freedom will be

[gmx-users] Free energy perturbation for larger molecule - big Coulomb solvation energies

Hello! I am trying to calculate solvation energy, using Free Energy Perturbation for lutein in water and bilayer. Simulation runs smoothly, but Coulomb part of calculated energy is extremly high for hydrophobic molecule (C40H54(OH)2): above 40kcal/mol // 180 kJ/mol both in water and bilayer. I am

Re: [gmx-users] RESTARTING THE CALCULATION

Hi, Then maybe the file is corrupted. What does gmx check say about it? Mark On Mon, Mar 12, 2018, 17:45 Neha Gupta wrote: > Hi, > > I gave > > gmx mdrun -s md.tpr -cpi md_step17960400.cpt > > It says, Checkpoint file corrupted or truncated or you are out of disk >

Re: [gmx-users] RESTARTING THE CALCULATION

Hi, I gave gmx mdrun -s md.tpr -cpi md_step17960400.cpt It says, Checkpoint file corrupted or truncated or you are out of disk space? I have deleted files of higher MB. Why the problem persists? Thanks, Neha On Sun, Mar 11, 2018 at 10:55 PM, Mark Abraham wrote: >

Re: [gmx-users] Problems in putting restraints during free energy perturbation calculations

Hi Mark, Thanks for reminding me about this. Yes, I've read up on this on a tutorial and I probably interchanged which interactions should be turned on first. Thank you again. Have a wonderful day! Searle On Mon, Mar 12, 2018 at 12:32 PM, Mark Abraham wrote: > Hi, >

Re: [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

Hi, Yes, you can specify which energy-group pairs get which tables, and which do not get any (thus get the normal thing). Did you check out the documentation yet? Mark On Mon, Mar 12, 2018 at 5:30 PM Debdas Dhabal wrote: > Hello everyone, > > Could anyone of you help

Re: [gmx-users] Problems in putting restraints during free energy perturbation calculations

Hi, Don't do that. You have charges on atoms that have no VDW, so there is nothing to stop them flying all over the place and imparting crazy forces on other atoms that have VDW, etc. Turn the VDW fully on before adding any charge. This is a fairly well known issue but something that people

Re: [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

Hello everyone, Could anyone of you help me regarding the aforementioned problem. It would be very nice of you. Thanks in advance. With regards Debdas On Sat, Mar 10, 2018 at 1:30 PM, Debdas Dhabal wrote: > Dear Mark, > > Thanks so much for your prompt reply. I had

[gmx-users] Problems in putting restraints during free energy perturbation calculations

Good day! I am doing some free energy perturbation to calculate the free energy of binding of an ion to a peptide. For one of my processes, I am slowly turning on the coulombic interactions by an increment of 0.05 lambda, followed by turning on the van der Waals interactions by an increment of

Re: [gmx-users] rvdw and rcoulomb

Note that rcoulomb, unlike rvdw, when using a PME long-range electrostatics, is tunable (together with the PME grid spacing). -- Szilárd On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul wrote: > > > On 3/11/18 7:33 PM, Ahmed Mashaly wrote: >> >> Dear users, >> Can I reduce the

Re: [gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?

Two things I forgot: - Ryzen chipsets are limited in the number of PCIE lanes, so if you plug in a second card (e.g. IB), you'll get x8 on both, which means GPU transfers will be slower too. Now, this may not be a great issue if you run multiple ranks per GPU which will provide some

Re: [gmx-users] Decrease position restraints force constant on the fly

Hi Zheng, No, I'm not trying to do steered MD, but rather step by step release my protein backbone atoms from position restraints. Thanks, both of you! Best wishes, Dawid 2018-03-12 15:47 GMT+01:00 Zheng Ruan : > Hi Dawid, > > If I understand correctly, you may able to

[gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?

Dear Gromacs users, I am currently working on a coarse-grained model where I want to fix atoms (Cb's) on a certain distance from Ca-Ca bonds, so that they can rotate freely. This freedom will be restricted by a dihedral that determines the relative orientation between the Cb's. I am using

Re: [gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?

Hi, Note that it matters a lot how far you want to parallelize and what kind of runs would you do? 10 GbE with RoCE may well be enough to scale across a couple of such nodes, especially if you can squeeze PME into a single node and avoid the MPI collectives across the network. You may not even

Re: [gmx-users] Decrease position restraints force constant on the fly

Hi Dawid, If I understand correctly, you may able to control the restraint using plumed. Check the "Moving on a more complex path" in this tutorial ( https://plumed.github.io/doc-v2.3/user-doc/html/belfast-5.html). Ruan On Mon, Mar 12, 2018 at 10:38 AM, Justin Lemkul wrote: >

Re: [gmx-users] Help with interpreting message for fatal error

Hi Viveca, Could you share more details of your simulations that may shed any light?  I assume that you are using parmbsc1 as the DNA forcefield.  Is it an "unusual" system?  We (and I am sure others) simulate DNA (± ligand) quite a bit and would be as interested in understanding what is

Re: [gmx-users] Help with interpreting message for fatal error

On 3/12/18 10:42 AM, Viveca Lindahl wrote: Hi Gregory, In the sense that I see it happening repeatedly yes :) But I can't reproduce it very predictably. After seeing that (for my small system) I get very large box vector fluctuations using Parrinello-Rahman, my current assumption is that

Re: [gmx-users] -sep option

On 3/10/18 4:52 PM, Mansoureh Shahbazi wrote: Dear justin, I want to make pdb files with regular intervals from a long trajectory. Can you please tell me an example command line using -sep? I want to get 100 pdbs from a 100 ns trajectory with 1ns (1000 ps) intervals. It's much easier with

Re: [gmx-users] seeming paradox with gmx wham

On 3/11/18 8:05 PM, Alex wrote: Just to add to my question... The pull code for the umbrella sampling from each of the N configs, as used in Justin's tutorial, is pull_coord1_type    = umbrella pull_coord1_geometry    = distance ... pull_coord1_dim = N N Y So, in each of the

Re: [gmx-users] rvdw and rcoulomb

On 3/11/18 7:33 PM, Ahmed Mashaly wrote: Dear users, Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind Regards,Ahmed These values are a function of the force field and are not freely tunable. -Justin -- == Justin A. Lemkul,

Re: [gmx-users] Help with interpreting message for fatal error

Hi Gregory, In the sense that I see it happening repeatedly yes :) But I can't reproduce it very predictably. After seeing that (for my small system) I get very large box vector fluctuations using Parrinello-Rahman, my current assumption is that there are some stability assumptions made by mdrun

Re: [gmx-users] NPT equilibration failing at high temperature

On 3/12/18 3:42 AM, Joe Jordan wrote: You should use the hint in the error message, that the system is not well equilibrated. Try a shorter time step or a double precision minimization. Also see

Re: [gmx-users] Easiest way to calculate the POTENTIAL ENERGY of a single isolated chain in GROMACS

On 3/12/18 9:37 AM, sanjeet kumar singh ch16d012 wrote: Hello list, Can anyone please tell me about how can i calculate the POTENTIAL ENERGY of a single isolated chain in the most easiest way in GROMACS. Generate a topology, .tpr, and use mdrun -rerun to evaluate the energy of a

Re: [gmx-users] Strange jumps in box dimensions

On 3/12/18 10:27 AM, Igor Ariz wrote: Hi all, I am simulating a small membrane protein system: Protein  1 (256 aminoacids) DPPC    104 SOL    4377 CL    7 NA    1 using CHARMM36m force-field, short cut-offs (0.9 nm) and semi-isotropic Berendsen p-coupling. Short cutoffs can lead to bad

Re: [gmx-users] Decrease position restraints force constant on the fly

On 3/12/18 10:37 AM, Dawid das wrote: Dear Gromacs Users, Is possible to decrease force constant for position restraints as the MD simulation progresses? For instance I start with 1000 kJ/(mol *nm2) and after 20 ps I go to 800 kJ/(mol*nm2), then after 20 ps to 600 kJ/(mol*nm2), etc.? No,

[gmx-users] Decrease position restraints force constant on the fly

Dear Gromacs Users, Is possible to decrease force constant for position restraints as the MD simulation progresses? For instance I start with 1000 kJ/(mol *nm2) and after 20 ps I go to 800 kJ/(mol*nm2), then after 20 ps to 600 kJ/(mol*nm2), etc.? Best wishes, Dawid Grabarek -- Gromacs Users

[gmx-users] Strange jumps in box dimensions

Hi all, I am simulating a small membrane protein system: Protein  1 (256 aminoacids) DPPC    104 SOL    4377 CL    7 NA    1 using CHARMM36m force-field, short cut-offs (0.9 nm) and semi-isotropic Berendsen p-coupling. I am experiencing sudden jumps in box dimensions from [6.52 6.52 6.96]

Re: [gmx-users] Comm-mode

Thank you very much. On Mar 12, 2018 14:51, "Justin Lemkul" wrote: > > > On 3/12/18 9:48 AM, Amin Rouy wrote: > >> Ahan, thanks Justin. Is it default in all versions of Gromacs? >> > > As far as I remember, yes, but don't take my word for it. Look at > mdout.mdp from grompp -

Re: [gmx-users] Comm-mode

On 3/12/18 9:48 AM, Amin Rouy wrote: Ahan, thanks Justin. Is it default in all versions of Gromacs? As far as I remember, yes, but don't take my word for it. Look at mdout.mdp from grompp - it has the full list of every setting that's being used in your simulation (and also the top of

Re: [gmx-users] Comm-mode

Ahan, thanks Justin. Is it default in all versions of Gromacs? On Mon, Mar 12, 2018 at 2:44 PM, Justin Lemkul wrote: > > > On 3/12/18 9:31 AM, Mark Abraham wrote: > >> Hi, >> >> Very many things are often simplified when you make a tutorial. Those .mdp >> files are already

Re: [gmx-users] Comm-mode

On 3/12/18 9:31 AM, Mark Abraham wrote: Hi, Very many things are often simplified when you make a tutorial. Those .mdp files are already complicated enough for a beginner. Indeed, and comm-mode = linear is the default behavior, so it works just fine without bothering the user to think

[gmx-users] Easiest way to calculate the POTENTIAL ENERGY of a single isolated chain in GROMACS

Hello list, Can anyone please tell me about how can i calculate the POTENTIAL ENERGY of a single isolated chain in the most easiest way in GROMACS. Cheers, SK -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] gmx potential calculation with one sodium ion at the center of box

Dear Gromacs users, I’m testing a simple system that has one sodium ion to check electric field. (NVE simulation) I used gmx potential- to check electric field. According to gromacs manual 5.0.4 (p.8), ‘the potential of an electronic charge at distance of 1nm equals f ~140 units ~ 1.4V.’

Re: [gmx-users] Comm-mode

Hi, Very many things are often simplified when you make a tutorial. Those .mdp files are already complicated enough for a beginner. Mark On Mon, Mar 12, 2018 at 2:26 PM Amin Rouy wrote: > But, why in some Gromacs tutorial there is no comm-mode used in .mdp file, > for

Re: [gmx-users] Comm-mode

But, why in some Gromacs tutorial there is no comm-mode used in .mdp file, for example in 'Lysozyme in water'; http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html On Mon, Mar 12, 2018 at 1:50 PM, Mark Abraham wrote: > Hi, > > If

Re: [gmx-users] Comm-mode

Hi, If you get this wrong, the equipartition of energy is usually broken and the simulation is probably unphysical. Mark On Mon, Mar 12, 2018, 13:47 Amin Rouy wrote: > Dear Justin, > > If we do not use comm-mode, which quantity might be changed after > simulations? > >

Re: [gmx-users] Help with interpreting message for fatal error

Since there hasn't been any response to your question yet, may I ask: is it reproducible? Gregory On 3/11/2018 7:30 AM, Viveca Lindahl wrote: Hi, I'm running a simulation of a periodic DNA molecule. After some time I get, sometimes the following error message: --- A list of

Re: [gmx-users] How to define ligand / metal atoms in gbsa.itp file of a force field for implicit MD??

Hi, On Mon, Mar 12, 2018 at 10:11 AM Vishwambhar Bhandare wrote: > Dear users, > > I want to perform implicit simulation for a protein-ligand complex. > for a protein alone, implicit works fine, but for ligand atoms it shows > error as copied below, > > Setting gen_seed to

[gmx-users] Fw: -sep option

Sent from Yahoo Mail on Android - Forwarded Message - From: "Mansoureh Shahbazi" To: "gmx-us...@gromacs.org" , "Justin Lemkul" Cc: Sent: Sun, Mar 11, 2018 at 1:22 Subject: Re: [gmx-users] -sep option Dear

[gmx-users] How to define ligand / metal atoms in gbsa.itp file of a force field for implicit MD??

Dear users, I want to perform implicit simulation for a protein-ligand complex. for a protein alone, implicit works fine, but for ligand atoms it shows error as copied below, Setting gen_seed to -1914387900 Velocities were taken from a Maxwell distribution at 300 K GB parameter(s) missing or

Re: [gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?

Hi, GROMACS doesn't much care about bandwidth, but rather message latency and message injection rate (which in some cases depends on what else is sharing the network). For those, even high quality gigabit ethernet *can* be good enough, so likely any Infiniband product will be just fine.

Re: [gmx-users] Minimal PCI Bandwidth for Gromacs and Infiniband?

Hi everyone, Our group is also interested in purchasing cloud GPU cluster. Amazon only supplies GPU cluster connected by 10Gb/s bandwidth. I notice this post but there is no reply by far. It would be nice if someone give any clue. Regards, Simon 2018-03-06 1:31 GMT+08:00 Daniel Bauer

Re: [gmx-users] NPT equilibration failing at high temperature

You should use the hint in the error message, that the system is not well equilibrated. Try a shorter time step or a double precision minimization. Also see

[gmx-users] NPT equilibration failing at high temperature

Hi I am trying to simulate a system contains two identical protein chains. I am equilibrating the system at 7 different temperatures. All the nvt ones have completed without any errors. 5 npt ones are also completed but in case of two highest temperatures 679.35 k and 800.0 k it is showing this