Re: [gmx-users] System volume "jumps" on exact continuations

Hi, Indeed, the evidence of abrupt volume changes in your later posts are rather more suggestive of a code problem. I suggest you open an issue at https://redmine.gromacs.org, and attach a tarball of files associated e.g. with

Re: [gmx-users] tetrahedral order parameter

I have used gmx hydorder but unable to understand the output as it gives two .xpm and two .out file. what these file describe please help. On Thu, Jun 1, 2017 at 6:14 PM, Justin Lemkul wrote: > > > On 6/1/17 3:42 AM, ISHRAT JAHAN wrote: > >> Dear all, >> I want to calculate

Re: [gmx-users] AMBER LIPID14 ff in GROMACS

Possibly build in amber and then convert to gromacs input format with parmed: https://github.com/ParmEd/ParmEd/issues/631 Looks like it might be a little tricky and of course you'd want to compare single-point energied in amber and then in the gromacs port, though that is complicated by code

[gmx-users] How to improve the performance of simulation in HPC (finding optimal number of nodes and processors)

Dear users, I am simulating a protein having 285 residues in a Gromacs environment installed in our University's HPC. Gromacs version: gmx, version 2016.3. I have tried to run the simulation using the standard "select=1:ncpus=28:mpiprocs=28" provided by our HPC admin (in pbs script). The same

Re: [gmx-users] Umbrella sampling and PMF calculations

> > >> > Your situation is completely different. Look into the cylinder settings > for dealing with a layered system, but I have no experience with them. To > be clear - you always need two groups to define the vector (reaction > coordinate) along which the bias is applied. So you need to

Re: [gmx-users] Umbrella sampling and PMF calculations

On 6/1/17 6:16 PM, Alex wrote: Your situation is completely different. Look into the cylinder settings for dealing with a layered system, but I have no experience with them. To be clear - you always need two groups to define the vector (reaction coordinate) along which the bias is

[gmx-users] How to conserve total energy from a position-restrained step to a non-constrained step

Hi all, So I've noticed that the total energy of my system decreases every time I run an un-constrained production run immediately after a position-restrained heating step, most likely due to algorithms. I am attempting to string together multiple repeated steps of heating and running, and

Re: [gmx-users] Doubt about gmx wham analysis

Dear Justin, Since I have the settings pull_coord1_dim = Y Y Y, I am not sure which axis the ligand is pulled. My initial simulation box size was 5 nm in each side. To care of the pulling of the ligand in any direction I made the box size 14 in each direction filled with water. The simulation

Re: [gmx-users] Umbrella sampling and PMF calculations

> > >> > You have a membrane with water on either side, yes? That's a layered > system. > > But frankly, at this point I don't follow at all what you're trying to do. > > - Let me try from the beginning. :) A membrane in XY, water on both sides. At the center of the membrane, there is a

Re: [gmx-users] charmm36 lipid forcefield error

On 6/1/17 4:43 PM, Archana Sonawani-Jagtap wrote: Hi, I want to perform GPCR simulation in POPC bilayer using Charmm36 forcefield. I have generated the bilayer using CHARMM-GUI. I am following GPCR tutorial by Justin (modified to GPCR by Anirban). CHARMM-GUI gives you the required force

Re: [gmx-users] Umbrella sampling and PMF calculations

On 6/1/17 4:28 PM, Alex wrote: Just a few quick questions for Justin. I am looking at your tutorial, starting here: http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html 1. In your example, you have two pull groups. My understanding is that both are pulled

Re: [gmx-users] How to calculate number of cholesterol molecules

On 6/1/17 4:27 PM, Archana Sonawani-Jagtap wrote: Hi, I want to perform atomistic simulation in POPC bilayer with 30% cholesterol. So I want to know how to calculate number of cholesterol molecules for 30% concentration? Depends on what the percentage means (and often the literature is

Re: [gmx-users] System volume "jumps" on exact continuations

On Thu, Jun 1, 2017 at 9:39 PM, Elizabeth Ploetz wrote: >>> However, if most runs are group scheme, a quick check could show whether >>> jumps are present in runs that i) do PP-PME tuning ii) if logs go truncated >>> during continuation at least whether they do use separate PME

[gmx-users] tetrahedral order parameter

Dear all, I want to calculate tetrahedral order parameter of water molecule.can anyone tell me how to calculate it. Thanks in advance -- 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] Third column of the " hbnum.xvg " file?...What is it meant for ?

On 6/1/17 11:02 AM, Erik Marklund wrote: Hi Mark, Exactly. But we want to phrase it such that it is legible in the legend if the file is plotted. I think we should adjust the help description in a manner like I suggested before (or more verbose if needed) and perhaps change the legend to

Re: [gmx-users] please help clarifying units for potential energy and enthalpy from gmx energy

Hi, I'm not sure, but I think David van der Spoel implemented these, so perhaps we should invite his input specifically. Mark On Thu, Jun 1, 2017 at 5:44 PM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > I am now presuming that the enthalpy is reported in kJ/mol where /mol > means

Re: [gmx-users] AMBER LIPID14 ff in GROMACS

On 6/1/17 12:50 PM, Amit Singh wrote: Hello Mark, Thank you very much for your prompt reply. Recently, Pluhackova K. *et al have *reported a work *(Ref: "A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers" **DOI* *:

Re: [gmx-users] please help clarifying units for potential energy and enthalpy from gmx energy

I am now presuming that the enthalpy is reported in kJ/mol where /mol means "per mole of simulation unit cells". That seems fine to me. I still think it's strange that the potential energy, but not the enthalpy, output by gmx energy is affected by the -nmol option, but perhaps that's for some

Re: [gmx-users] "cmake" failed to install

Dear Mark and Mario, Thank you very much. I delete the gromacs and redo the cmake and it works now. Yours sincerely Cheng -- Original -- From: "mario";; Date: Thu, Jun 1, 2017 04:07 PM To: "ZHANG Cheng"<272699...@qq.com>; Cc:

Re: [gmx-users] AMBER LIPID14 ff in GROMACS

Hello Mark, Thank you very much for your prompt reply. Recently, Pluhackova K. *et al have *reported a work *(Ref: "A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers" **DOI* *: 10.1021/acs.jpcb.6b01870) related to the use of

[gmx-users] "cmake" failed to install

Dear Gromacs, I did the below on Ubuntu 14.04: tar xfz gromacs-5.1.4.tar.gz cd gromacs-5.1.4 mkdir build cd build Then, I got error message when running: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON The error log files can be found here:

Re: [gmx-users] Simulated annealing

Hi, Simulated annealing for system preparation is a waste of time in my opinion. Recommended simulation preparation protocols are on the Gromacs website, and are all you need unless your starting conformation has serious problems, and then simulated annealing may or may not help Mark On Wed, 31

[gmx-users] Disparity in total energy between consecutive steps

Hi all, So I've been trying a series of runs of heating-active-site-of-protein, then NVE, then heating again, and NVE again. And I've seemed to notice that the total energy of the system between the end of the heating process and the beginning of a NVE step right after it is significantly

Re: [gmx-users] "cmake" failed to install

Dear Cheng: I solved that problem by following step by step instructions of the next page: https://bioinformaticsreview.com/20151126/how-to-install-gromacs-5-x-x-on-linux-ubuntu-14-04-lts/ Best Regards Mario Campo Dpto Física - UNLPam La Pampa Argentina > Dear Gromacs, > I did the below on

Re: [gmx-users] Deuterium Order Parameter Calculations

On 5/31/17 11:35 AM, Sanim Rahman wrote: Thank you Justin, That makes much more sense. I was able to fix the error. I have one more question that is out of topic from the original question. Is there a guide that informs the user on what index groups should be made for each type of analysis? I

Re: [gmx-users] tetrahedral order parameter

On 6/1/17 3:42 AM, ISHRAT JAHAN wrote: Dear all, I want to calculate tetrahedral order parameter of water molecule.can anyone tell me how to calculate it. Use gmx hydorder -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA

Re: [gmx-users] Doubt about gmx wham analysis

On 5/31/17 10:49 AM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, During the pulling part of the umbrella sampling for finding binding affinity of the Protien-ligand system, the ligand(peptide) is deformed and its helices straighten along with large conformational changes in Protein.

Re: [gmx-users] DrudeFF topology transfer from CHARMM to GROMACS

Thank you, Justin. That solves my problem. Best, Tomasz K. Piskorz On 31 May 2017 at 13:51, Justin Lemkul wrote: > > > On 5/31/17 7:06 AM, Tomasz Piskorz wrote: > >> Dear all, >> >> I would like to simulate cyclohexane using Drude FF in GROMACS. I've seen >> that the

Re: [gmx-users] "cmake" failed to install

Hi, We can't see the error message you got on the terminal, so we don't know what the problem is. Mark On Thu, Jun 1, 2017 at 12:50 PM ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs, > I did the below on Ubuntu 14.04: > > > tar xfz gromacs-5.1.4.tar.gz > cd gromacs-5.1.4 > mkdir build >

Re: [gmx-users] Reg: creation of separate chains in .pdb file

On 6/1/17 4:30 AM, Syed Azeem wrote: On 5/31/17 8:26 AM, Syed Azeem wrote: On 5/29/17 8:00 AM, Syed Azeem wrote: Hey all, I simulated a protein-peptide docked complex. Post simulation, I created an index file selecting only the Protein Group (protein-peptide complex). Then using editconf, I

Re: [gmx-users] REMD analysis of trajectories

Hi, That's what you already have. See http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing Mark On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283...@163.com> wrote: > Hi, >I have run a 100ns-REMD of protein, which has 20 replicas (i.e. > remd1.xtc, remd2.xtc, ...,

Re: [gmx-users] System volume "jumps" on exact continuations

On Thu, Jun 1, 2017 at 9:39 PM, Elizabeth Ploetz wrote: > However, if most runs are group scheme, a quick check could show whether > > jumps are present in runs that i) do PP-PME tuning ii) if logs go truncated > during continuation at least whether they do use separate PME ranks

[gmx-users] charmm36 lipid forcefield error

Hi, I want to perform GPCR simulation in POPC bilayer using Charmm36 forcefield. I have generated the bilayer using CHARMM-GUI. I am following GPCR tutorial by Justin (modified to GPCR by Anirban). I want to remove periodicity of the generated bilayer using following command: grompp -f EM.mdp

[gmx-users] System volume "jumps" on exact continuations

However, if most runs are group scheme, a quick check could show whether jumps are present in runs that i) do PP-PME tuning ii) if logs go truncated during continuation at least whether they do use separate PME ranks (because otherwise CPU-only runs don't tune). i) If grepping "timed" from the

[gmx-users] How to calculate number of cholesterol molecules

Hi, I want to perform atomistic simulation in POPC bilayer with 30% cholesterol. So I want to know how to calculate number of cholesterol molecules for 30% concentration? Thanks and Regards, Archana Jagtap PhD student Mumbai, India. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Umbrella sampling and PMF calculations

Just a few quick questions for Justin. I am looking at your tutorial, starting here: http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html 1. In your example, you have two pull groups. My understanding is that both are pulled relative to each other. In my case,

[gmx-users] gmx trjconv -center -boxcenter zero isn't amazing at putting the selection at (0, 0, 0), but I don't know why

Dear Users: Using gmx 5.1.2, I find that centering a selection of the system at (0,0,0) works better via "editconf -c -center 0 0 0" than it does via "trjconv -center -boxcenter zero" here's the comparison of the center of mass of the selection centered in these two different ways: TRJCONV:

Re: [gmx-users] System volume "jumps" on exact continuations

> Hi, > > Thanks for the report. > > On Wed, May 31, 2017 at 4:56 PM Elizabeth Ploetz wrote: > >> Dear GMX-USERS, >> >> We are observing abrupt, discontinuous “jumps” in our simulation box >> volume for different chunks of trajectory when performing exact >> continuations of

Re: [gmx-users] System volume "jumps" on exact continuations

1. Once you identify a continuation (with associated run script) that gives the discontinuity, if you run many repeats of the original continuation then does the jump always occur or only sometimes? The jumping does not always occur. See the linked

Re: [gmx-users] REMD analysis of trajectories

Do you mean that the original trajectories REMD generated are belong to "one trajectory per temperature" (i.e. the md2.xtc is a trajectory at 298K)? Ouyang At 2017-06-01 21:00:52, "Mark Abraham" wrote: >Hi, > >That's what you already have. See

Re: [gmx-users] "cmake" failed to install

After following Mario's link, I still could not solve it. The same problem happens. My command line is: lee@ubuntu:~/Jef/gromacs/gromacs-5.1.4/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- The CXX compiler identification is GNU 4.8.4 -- Check for working CXX

Re: [gmx-users] "cmake" failed to install

Hi, I don't think that cmake command can produce that result. Please remove everything from the build directory and run that cmake command again. I would also investigate why your compiler versions are mismatched. If you are using the compilers provided by Ubuntu, then this is wildly unlikely to

Re: [gmx-users] "cmake" failed to install

Seems to be an old problem. You should read this https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097312.html > After following Mario's link, I still could not solve it. The same problem > happens. > > > My command line is: > > > lee@ubuntu:~/Jef/gromacs/gromacs-5.1.4/build$

Re: [gmx-users] System volume "jumps" on exact continuations

Hi, Thanks for the report. On Wed, May 31, 2017 at 4:56 PM Elizabeth Ploetz wrote: > Dear GMX-USERS, > > We are observing abrupt, discontinuous “jumps” in our simulation box > volume for different chunks of trajectory when performing exact > continuations of standard, explicit

Re: [gmx-users] gmx freevolume

Hi, I have no idea, but David van der Spoel implemented this tool, so perhaps forward your gmx-users query to him personally? Mark On Mon, May 29, 2017 at 3:43 PM Federico Gallino < federico_gall...@saes-group.com> wrote: > Dear All, > > I would like to put your attention on the output of gmx

[gmx-users] Analysis

I have few doubts in MD analysis. *How to calculate the deviation angle between two helix of a protein? (for every ns) or in other words how can I know whether the two helices (consecutive) have moved apart during simulation? *In saltbridge analysis how can I eliminate CL and NA ions? (Before

Re: [gmx-users] AMBER LIPID14 ff in GROMACS

Hi, I'm not aware of anybody who's done this. It's a lot of work to produce both the conversion and run a verification suite, which as far as I know the AMBER forcefield developers don't make available even for AMBER simulation package users. Mark On Wed, May 31, 2017 at 6:49 PM Amit Singh

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

Yes. The sets have no overlap. But for some reason putting that in a short description seems difficult :-) > On 1 Jun 2017, at 15:31, Mark Abraham wrote: > > Hi, > > I still don't understand your description. Is the third column *additional* > pairs within 0.35 that

Re: [gmx-users] How to perform final MD simulation after extending a NPT simulation

Hi On Wed, May 31, 2017 at 2:50 AM Adarsh V. K. wrote: > Dear all, > > *I used following command to extend a NPT simulation* > > gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr > gmx mdrun -deffnm tpxout -cpi npt_prev.cpt -v > If the npt run was long enough,

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

Hi, I still don't understand your description. Is the third column *additional* pairs within 0.35 that do not satisfy the angle criterion? Mark On Sat, May 27, 2017 at 4:36 PM Erik Marklund wrote: > > > On 26 May 2017, at 22:12, David van der Spoel

Re: [gmx-users] Doubt about gmx wham analysis

Dear Justin, Gazillion thanks for the valuable insight! Best Regards, Bhagyesh - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Thursday, June 1, 2017 6:13:00 PM Subject: Re: [gmx-users] Doubt about gmx wham analysis On 5/31/17 10:49 AM,

Re: [gmx-users] "cmake" failed to install

On Thu, Jun 1, 2017 at 2:39 PM wrote: > Dear Cheng: > I solved that problem by following step by step instructions of the next > page: > > > https://bioinformaticsreview.com/20151126/how-to-install-gromacs-5-x-x-on-linux-ubuntu-14-04-lts/ That's a bit of a strange

Re: [gmx-users] REMD analysis of trajectories

Hi, What did you learn from the first sentence of the link I gave you? Mark On Thu, Jun 1, 2017 at 3:20 PM YanhuaOuyang <15901283...@163.com> wrote: > Do you mean that the original trajectories REMD generated are belong to > "one trajectory per temperature" (i.e. the md2.xtc is a trajectory

Re: [gmx-users] REMD analysis of trajectories

Ouyang, Each Replica corresponds to 1 temperature in Gromacs (unlike other software packages). If you want to have continuous trajectories (i.e. follow the motion of one replica through temperature exchanges) then you have to demux. But the demux is really only useful (in my experience) with

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

Hi Mark, Exactly. But we want to phrase it such that it is legible in the legend if the file is plotted. Erik On 1 Jun 2017, at 16:51, Mark Abraham > wrote: Hi, "Pairs within 0.35" has misled David, Justin and I, and doubtless