Re: [gmx-users] PBC after energy minimization

* For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. > John Whittaker Ph.D. Candidate Department of Mathematics and Computer Science Freie Un

Re: [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. John Whittaker Ph.D. Candidate

Re: [gmx-users] Double-well potential for bonded interaction

/www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. John Whittaker Ph.D. Candidate Depa

Re: [gmx-users] converting gromacs topology file to namd topology file

Hi, A quick google search led me to this: https://www.ks.uiuc.edu/Research/namd/2.10/ug/node14.html I've never used NAMD before but apparently you can use gromacs topologies directly in NAMD. Note the caveats at the bottom of the page. Would this work or does it not accomplish what you are

Re: [gmx-users] GROMACS automation

thing new. Best, - John > > Many Thankss > Mohamed > > On Thu, Mar 12, 2020 at 11:51 AM John Whittaker < > johnwhitt...@zedat.fu-berlin.de> wrote: > >> > I was planning to put the velocities in the .gro file from which I am >> > inserting the mo

Re: [gmx-users] GROMACS automation

> generated by gmx select (in this case, since you're specifying a >> geometric criterion). >> >> -Justin >> >> > Thanks for your reply. >> > Mohamed >> > >> > On Wed, Mar 11, 2020 at 13:43 John Whittaker < >> > johnwhitt...@

Re: [gmx-users] slurm and gromacs

This link should help: http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts - John > Dear gromacs users > > I am doing md simulation of protein in a cluster system with > Slurm Workload Manager using following job file: >

Re: [gmx-users] GROMACS automation

Write a script that calls gmx insert-molecules 3000 times and uses the previous output as input for each call. http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html Is there something you have to do in between each insertion? - John > Hello everybody, > > I am

Re: [gmx-users] Replicate a structure

> Then my command would be gmx genconf -f system.gro -nbox 2 1 1 -o > new_system.gro right?? Based on what you described, I'd say that's correct. Try it out and then visualize the resulting .gro file to see if things are how you want them to be. > > On Tue, Mar 10, 2020, 6:01 PM Jo

Re: [gmx-users] Replicate a structure

Probably better to use gmx genconf; This situation is probably its main purpose. - John > Gmx editconf you can use with -translate flag...after that merz the > coordinates of two water droplets. I hope this may help you. > > On Tue 10 Mar, 2020, 9:35 AM Devargya Chakraborty, < >

Re: [gmx-users] Could you help me deal with GC-AdResS approach implemented in Gromacs?

Hi Ekatherina, I currently develop AdResS (I am the successor to the post-doc who uploaded the files to the e-cam site) and would be happy to help, but since Gromacs no longer supports AdResS, perhaps we should continue the conversation off the user list. If you'd like to talk about the method or

Re: [gmx-users] error on graphene sheet simulation

Hi, That tutorial is not from the GROMACS team, it is provided by a user. Anyway, something is wrong with your topology. The CHARMM forcefield used in that tutorial has the atomtype CG2R61 available, so it should be defined in your topology as long as you include the CHARMM36 forcefield. Can

Re: [gmx-users] Umbrella sampling of peptide-membrane system

Hi, Justin's tutorial is not a fully generalized procedure for umbrella sampling; it shows a workflow for one specific example which is not always applicable to other systems. In general, you don't have to use position restraints for anything in umbrella sampling. Justin uses them to keep the

Re: [gmx-users] Experimental to Simulation Time Period Conversion

> Dear group members > > My sincere apologies for the non-Gromacs related question, but I require > this information urgently and hence posted my query here. > > Could someone please provide me with any guidelines to appropriately model > experimental processes with molecular dynamics simulations?

Re: [gmx-users] Analysis with .sh file

What is the command that causes the error and is the error due to incorrect syntax for bash or gromacs? No one will be able to help without more information. - John > Dear all, > > I have recently upgrade my Gromacs to the 2019 version from the 5.0.4 > and I found out that now that while I'm

Re: [gmx-users] Remove water molecules from .tpr file

Hi Navneet, You can probably delete the water molecules and ions from your .gro file and run all the necessary files through grompp again. This should generate a new dummy .tpr file you can use that matches your trajectory file. Best, John > Hello Everyone! > > I want to calculate the

Re: [gmx-users] GPU performance, regarding

Hi, > Hi Users. > > I am simulating a peptide of 40 residues with small molecules using oplsaa > ff in Gromacs 2018.20 installed in CUDA environment.. The workstation has > 16 Cores and 2 1080Ti card On execution of command gmx_mpi mdrun -v > -deffnm > md for 100ns it shows no usage of gpu card.

Re: [gmx-users] Question: How to delete water

To add on to your answer, Justin: The usage listed in the tutorial instructs you to use the "-nwater" flag to specify the number of atoms in a water molecule. The actual script uses "-water" as a flag, without the "n". I noticed this in a previous version of the script before the usage in the

Re: [gmx-users] Stochastic Dynamics nsttcouple

this note can be added to the documentation (at least the mdp options page)? Thanks again, John > > > On 11/6/19 10:40 AM, John Whittaker wrote: >> Hi all, >> >> Please correct me if this is the wrong list for this particular >> question. >> >> I have bee

[gmx-users] Stochastic Dynamics nsttcouple

Hi all, Please correct me if this is the wrong list for this particular question. I have been messing around with the stochastic dynamics integrator in version 5.1 (yes, it's relatively ancient, but I am testing some things involving AdResS) and I can't wrap my head around something: In the

Re: [gmx-users] error in Umbrella sampling

Hi, Without any information about the parameters you are using in your simulation, no one will be able to provide much help. I recommend reading and understanding this tutorial before you try to perform an umbrella simulation totally blind: http://www.mdtutorials.com/gmx/umbrella/index.html

Re: [gmx-users] Question about gmx_wham

Hi, > Hello, > > I am currently running Umbrella Sampling simulations on Vitamin E (in > grommacs version 4.6.5). And I followed the tutorial done by Justin A. > Lemkul, however I am uncertain of a few things about the gmx_wham command > that he instructs us to use. > > Namely for the two output

Re: [gmx-users] �ظ�: �ظ�: Re: Implicit Solvent and Box Size

Hi, As Justin mentioned, with implicit solvent, there is no "box". The solute is simply diffusing through space. The idea of a simulation box is only relevant when you are using PBC. Despite having box vectors present at the bottom of your .gro file, these don't really have a meaning if you're

Re: [gmx-users] Umbrella sampling on lipid bilayer

> Dear gromacs users, > > Sorry for repeating my question. > > I didn't receive any email so I couldn't reply and I missed > > them. Hi, Justin replied in this mail: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-September/126735.html Best, John > > I am using following

Re: [gmx-users] GROMACS Domain decomposition

> Dear gmx-users, > > Would you mind giving me some instruction on this. > > I am learning Gromacs tutorial #1 of mdtutotials.com. However to the 5th > step: EM, http://www.mdtutorials.com/gmx/lysozyme/05_EM.html > I got the error: > "Domain decomposition does not support simple neighbor

Re: [gmx-users] question on system blow-up

Hi, > Dear gmx-users, > > Could I ask a question on system blow-up? Thanks! > I finished em, nvt, and npt. But when I ran production(npt) 10ns, I found > system blow up at around 1ns. ("atoms involved moved further apart than > the > multi-body cut-off distance") > > When I checked the trajectory

[gmx-users] Direction-periodic confusion

Hi all, I performed some simple umbrella sampling simulations involving two peptides, after having increased the distance between them to about 6.5 nm, with the goal of deriving a PMF as a function of the absolute distance between them. In a stupid attempt to save resources, I created a long

Re: [gmx-users] RAM usage of gmx msd

Hi Martin, > Hello everyone. > > I simulated a cell membrane and would like to calculate lateral > diffusion of lipids. I tried this using the gmx msd command. > Unfortunately this uses enormous amounts of RAM. The process runs > without error until it is killed by the operating system. No

Re: [gmx-users] Delete Groups from gro file

Hi, You could use gmx trjconv: http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html You can use the index file to select only that subset of atoms from a single frame of your trajectory and output it as a new .gro file. Cheers, John > Hallo All, > > I have a big gro file

Re: [gmx-users] wham analysis

Hi, > >  Dear all,I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS > Tutorial ) for my file which is protein-ligand complex. > The pulling force was in Y direction. when Umbrella sampling finished, > "Wham" couldn't analysis the data because wham is in z direction.what > should I

Re: [gmx-users] Fwd: Simulation blowing up in parallel (h-bonds constraints)

Hi Jan, > Dear gromacs-users, > > I am encountering a puzzling problem with my simulation of a simple > protein (~2.000 atoms, only standard amino acids, Calcium cofactor) in > tip3p water (~10.000 molecules) using the amber99sb-ildn force field and > lincs constraints set to "h-bonds". When I

Re: [gmx-users] WARNING

If your trajectory has position information, then yes, it can be used to compute potential energies. > Thank you for your reply sir. In this case can I use .The file to compute > potential energies. > > On Tue 20 Aug, 2019, 4:40 PM Mark Abraham, > wrote: > >> Hi, >> >> You're doing a rerun from

Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

> Hi Justin, > > Yes, I'm using a queuing system with a submission script. > > #-l nodes=1:ppn=16 > > #PBS -l walltime=10:00:00 > > #PBS ­-qmedium > > #PBS -N NVT > > #PBS -e out.err > > #PBS -o out > > > > module load gromacs > > > cd ${PBS_O_WORKDIR}/; > > > gmx mdrun -deffnm nvt > > > Well,

Re: [gmx-users] simulation continuation - gen-vel = yes

Thank you, Mark. That makes me feel better. - John > Hi, > > gen-vel is interpreted by grompp, never mdrun. > > Mark > > On Thu., 13 Jun. 2019, 13:04 John Whittaker, < > johnwhitt...@zedat.fu-berlin.de> wrote: > >> Hi all, >> >> I have a simple

[gmx-users] simulation continuation - gen-vel = yes

Hi all, I have a simple question that I hope someone can answer. When I began my simulation, my .mdp file had "gen-vel = yes" in order to generate some initial velocities. My next simulation was a continuation of the first (I am setting nsteps = -1 and running mdrun with the flag -maxh in order

Re: [gmx-users] Running gromacs analysis on a HPC

Hi Akash, Take a look here: http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts Alternatively, I think you could also do something like: echo "1" > select; echo "12" >> select; gmx rdf -s proteinwater.tpr -f proteinwater.xtc -o proteinwaterrdf.xvg -bin 0.002 -norm rdf

Re: [gmx-users] Timestep in GROMACS simulation

Hi, > I'm still not clear what "sampling" means. Does it mean collecting data > from the simulation? Pretty much. The point of a molecular dynamics simulation is to calculate structural, thermodynamic, etc... properties of some system from the microscopic dynamics of atoms/molecules/whatever.

Re: [gmx-users] Restart dynamics when trr files removed

Hi, > But NO - I can't restart the simulation from 50 ns on without trr files There should be a checkpoint file called (by default) state.cpt that was generated when your 50 ns simulation finished. You can use this file to continue your run from the final state of that simulation with: gmx

Re: [gmx-users] TIP4P molecules stuck together

said makes sense. I appreciate the help. John > On Thu, May 9, 2019 at 8:43 AM John Whittaker < > johnwhitt...@zedat.fu-berlin.de> wrote: > >> Hi all, >> >> I have a rather strange question that I hope someone can shed some light >> on. >> >>

[gmx-users] TIP4P molecules stuck together

Hi all, I have a rather strange question that I hope someone can shed some light on. Before I begin, I want to note that I am pioneering some new developments of the Adaptive Resolution Simulation technique (https://doi.org/10.1002/adts.201900014), so the simulations/techniques I am

Re: [gmx-users] Initial velocities before equilibration

Hi, > After completing MD production run, I ran a command gmx check for my xtc > file. However, no velocities were updated in any frame. http://manual.gromacs.org/documentation/2016/user-guide/file-formats.html The .xtc trajectory filetype does not support velocities or forces, only positions.

Re: [gmx-users] increase membrane dimensions

Sorry for the double post, but you could also try using CHARMM-GUI. http://www.charmm-gui.org/ That way you don't have to deal with implementing the Berger lipids into the gromos force field (note that CHARMM is all-atom while gromos is united-atom). I have only used it to make a pure lipid

Re: [gmx-users] increase membrane dimensions

Hi Emilio, > Is there a way of doing it using gromacs tools? Perhaps you can use gmx genconf? http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-genconf.html Have a look and see if it would work for you. I'm sure there are other ways that may be better, but this is the first that

Re: [gmx-users] Settings of SD integrator

Hi, Apramita > For these simulations, the papers suggest the SD integrator. > But mdp options for SD integrator is not defined clearly > I've included ld_seed > tried changing the tau_t > Could anyone tell me what correct mdp options are required to be changed > while using SD integrator? Have

Re: [gmx-users] gmx do_dssp

> but I don't know what those letters (E, S H etc) means. I haven't used DSSP analysis in GROMACS but I have in AMBER, so I assume the letters indicate the type of secondary structure for each residue as given below: "The output of DSSP is explained extensively under 'explanation'. The very

Re: [gmx-users] Error in NVT equilibration step

> Fatal error: > There is no domain decomposition for 48 ranks that is compatible with > the > given box and a minimum cell size of 3.33469 nm > Change the number of ranks or mdrun option -rdd or -dds > Look in the log file for details on the domain decomposition > > Is there anyone who nows what

[gmx-users] Area compressibility modulus GMX

Hi all, I have a weird, probably very basic question to ask and I hope it is appropriate for the mailing list. I am trying to reproduce the pure DPPC bilayer data found in J. Chem. Theory Comput., 2016, 12 (1), pp 405–413 (10.1021/acs.jctc.5b00935) using the recommended protocol given in the

Re: [gmx-users] CHARMM36 GROMACS implementation

explanation for why this might happen? Thanks again in advance for any help. John > > > On 11/19/18 11:32 AM, John Whittaker wrote: >> Hi all, >> >> I am trying to reproduce the pure DPPC bilayer data found in J. Chem. >> Theory Comput., 2016, 12 (1), pp

[gmx-users] CHARMM36 GROMACS implementation

Hi all, I am trying to reproduce the pure DPPC bilayer data found in J. Chem. Theory Comput., 2016, 12 (1), pp 405–413 (10.1021/acs.jctc.5b00935) using the recommended protocol given in the paper. Recently, I realized I made a mistake and have been using the CHARMM36 forcefield provided by Tom