Re: [gmx-users] Calculate dihedrals

Hi, On Wed, Mar 25, 2020 at 1:10 PM Marko Petrovic wrote: > Hello > > I want to calculate som singular dihedral values and I know this is > simple, but can't figure out the usage of "gmx gangle" . I tried using "gmx > angle" but the results were not what I was hoping for as it calculates an >

Re: [gmx-users] No default bond types

Hi, On Wed, Mar 25, 2020 at 4:17 AM Neena Susan Eappen < neena.susaneap...@mail.utoronto.ca> wrote: > Hello gromacs users, > > I just modified opls force field for a modified aminoacid with 4 new bond > types and 9 new angle types. Which force field files have you modified? It looks that you

Re: [gmx-users] Extracting temperature of specific groups during the simulations

HI, On Wed, Mar 25, 2020 at 9:33 AM Mijiddorj B wrote: > Dear GMX users, > > I would like to extract the temperatures for specific groups during the > simulations. gmx energy gives the system temperature as a function of time. > I also tried to get the temperature of a specific group using gmx

Re: [gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities

Hi On Sat, Mar 21, 2020 at 3:20 AM Wesley Michaels wrote: > Hello, > > I hope this message finds you well! I'm running a pretty simple simulation > of a polyethylene melt (N = 100, 50 chains in the simulation, T = 500K, P = > 1atm, NPT ensemble, dt = 1 fs, OPLS-AA FF). My simulations are

Re: [gmx-users] alchemical free energy calculation with physical PBC

Hi, On Wed, Mar 18, 2020 at 4:52 PM Johannes Hermann wrote: > Dear all, > > I am calculating free energy changes with the alchemical free energy > framework provided in gromacs. My alchemical transformation involves a > charge change in a periodic system, where the periodicity is physical in >

Re: [gmx-users] About gmx msd and membrane leaflets

Hi, On Tue, Mar 17, 2020 at 11:15 PM Poncho Arvayo Zatarain < poncho_8...@hotmail.com> wrote: > > > Hello gromacs users: I want to obtain the lateral diffusion for a membrane > with approximately 55 lipids+ions (NA+Cl) but i want to this for each > leaflet of the membrane (outter and inner) and

Re: [gmx-users] makes sense for Ryckaert Bellemans dihs. only.

Hi, This may be the answer to your question https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2004-February/009490.html Best regards Alessandra On Mon, Mar 16, 2020 at 7:05 PM Sadaf Rani wrote: > Dear Gromacs users > > I am calculating a dihedral angle between certain atoms by

Re: [gmx-users] Parametrization of Mn(ii) in charmm force field

Hi, You have to search in literature for parameters for Mn ions compatible with CHARMM36 and with the water model (some ions are parameterized to reproduce structural, thermodynamics, kinetic properties in water solution). For example Mn non-bonded parameters can be found *J. Phys. Chem. A*

Re: [gmx-users] NVT.mdp running in 4.6 version but failed in VERSION 5.1.2

Hi, mdp option may have been changed going from 4.6 to 5.1 , you should update your mdp file according to the 5.1 option (see http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html ) If you do not have any special reason to use 5.1, I will suggest to move to the newest version

Re: [gmx-users] Clarification on the "-surface" and "-output" options of "gmx sasa"

On Mon, Mar 9, 2020 at 2:47 PM ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs, > > > There seems to be very little explanation on the "-surface" and "-output" > options of "gmx sasa": > -surface: This should always consist of all non-solvent atoms in the > system. The area of this group is

Re: [gmx-users] Amber14SB

Hi, Here a page of force field in GROMACS http://manual.gromacs.org/documentation/current/user-guide/force-fields.htm maybe it helps. I did not fully understand your question Best regards Alessandra On Tue, Mar 3, 2020 at 10:04 AM Eduardo Mayo wrote: > Hi!! > I'm sorry if is the amber14sb

Re: [gmx-users] Force field for urea and urea-TMAO mixture

Hi, The urea model of Lorna Smith ( https://pubs.acs.org/doi/abs/10.1021/jp030534x ) should be compatible with GROMOS force field. Best regards Alessandra On Wed, Mar 4, 2020 at 7:00 AM ISHRAT JAHAN wrote: > Dear all, > I want to do MD simulation of protein in urea and urea-TMAO mixture. Can >

Re: [gmx-users] PEG from ATB: No residues in chain

Hi, On Wed, Mar 4, 2020 at 4:11 PM Schirra, Simone wrote: > Dear Gromacs users, > > I'm totally new to GROMACS and I want to simulate a PEG chain in different > environment. I found various PEG topologies on the ATB website and tried to > use them combined with the force field provided on the

[gmx-users] regard emails on unsubscription from the gromacs.org_gmx-users mailing list

Dear all, Some of you have got a notification (yesterday around 7.30 am) that they have been unsubscribed from the gmx_user mailing list from gromacs.org_gmx-users-boun...@maillist.sys.kth.se. The reason is under investigation. In the meanlime, please re-subscribe to the mailing list via the

Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3

(will this just be the same as rcoulomb?) > > > Thanks again for your help. > > Best regards, > > Robert > > -Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf

Re: [gmx-users] Increase Graphene sheet size

imulated the graphene sheet but I need to increase its dimension > to a certain dimensions. > > any Ideas how to do that :) ? > > Thanks, > Mohamed > > On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa < > alessandra.villa.bio...@gmail.com> wrote: > > &g

Re: [gmx-users] Implementing the NERD Force Field in GROMACS 2019.3

HI, Below some suggestions assuming that the energy terms are correctly implemented (force field) On Tue, Feb 18, 2020 at 3:13 PM Robert Cordina wrote: > Hi, I’m trying to use the NERD forcefield (Sum et al. J. Phys. Chem. B > 2003, 107, 14443-14451) in GROMACS 2019.3 for a pure

Re: [gmx-users] How to cap a single residue in gromacs

Hi On Tue, Feb 18, 2020 at 4:30 PM Sadaf Rani wrote: > Dear Gromacs users > I am trying to make a system with 1 single amino acid(PHE) and 1 Ligand > when I run pdb2gmx it gives me error:- > Fatal error: > In the chosen force field there is no residue type for 'PHE' as a > standalone >

Re: [gmx-users] Tabulated potentials

.@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: maandag 17 februari 2020 9:34 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Tabulated potentials > > Hi, > On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari < &g

Re: [gmx-users] Increase Graphene sheet size

Hi On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal wrote: > Hello All, > > I want to create a graphene sheet with a specific dimensions (10*15*0.284) > nm. > > I created a .gro file as below ( as mentioned in this website > >

Re: [gmx-users] How to dynamically change the "pull-coord1-init" during SMD simulation

HI However, since I want to pull the protein for a long distance, I should > gradually change the equilibrium length, and I have no idea how to > dynamically change the "pull-coord1-init" during SMD simulation. Or do I > have to restart the simulation with a new .mdp file with different >

Re: [gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output

Hi, I guess that the reported energy are averaged over the simulation time. If you want to compare energies and understand what change in the topology implied, it is better to compare the energies of the first step using the same starting structure. The definition of LJ interactions (including

Re: [gmx-users] Cannot flush logfile - maybe you are out of disk space?

Hi, On Mon, Feb 17, 2020 at 7:48 AM Dilip.H.N wrote: > Dear all, > I have extended a simulation (extension for 50 ns) and after some time i > get the following error "Cannot flush logfile - maybe you are out of disk > space?" and now the simulation has stopped running. The log file of the >

Re: [gmx-users] Tabulated potentials

yone has any idea why it could be happening? > > My best, > Ali > > > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: donderdag 13 f

Re: [gmx-users] Tabulated potentials

Hi, On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < ali.khoday...@student.kuleuven.be> wrote: > Dear Gromacs users, > > I’ve got a question regarding the tabulated potentials for bonded > interactions. > > Gromacs recognises and reads the non-bonded potential tables through the > energy groups

Re: [gmx-users] Free energy perturbation of ligand

Hi, On Wed, Feb 12, 2020 at 8:54 AM TIASHA ADHIKARY wrote: > Hello, > I am trying to calculate FEP using gromacs. I have used pmx for initial > structure and .itp file. > I am getting the following warning > > WARNING 1 [file MOL.itp, line 185]: > Some parameters for bonded interaction

Re: [gmx-users] simulation on graphite sheet

Hi, On Tue, Feb 11, 2020 at 2:13 PM Devargya Chakraborty < devargyachakraborty@gmail.com> wrote: > Hello, > I was thinking of simulating a liquid on graphite surface and have made a > system but couldnt simulate it. while doing the nvt simulation, after some > time i am getting lincs error.

Re: [gmx-users] How to use LBFGS minimization

Hi, On Thu, Feb 6, 2020 at 10:39 AM Bratin Kumar Das < 177cy500.bra...@nitk.edu.in> wrote: > Dear all > I want to use LBFGS algorithm for minimizing my system..what > parameters is required for that...any suggestions or any tutorial is there > for that. > the mdp parameter for

Re: [gmx-users] Question about gromacs mailing list

Hi, On Thu, Feb 6, 2020 at 4:02 AM Amit Kumar wrote: > Dear gromacs users, > After subscribing to the gromacs mailing list I am getting only daily > digest, I am not getting a question-answer thread, so posting my question > once I cannot reply in the thread. > > You have probably selected

Re: [gmx-users] Fwd:

HI, Are you using a third-party tools for MMPBSA analysis? You could ask directly to the authors Best regards Alessandra On Wed, Feb 5, 2020 at 7:19 AM saranya wrote: > I have performed a simulation for a protein-metal cluster complex system > for 500ns. While calculating MMPBSA analysis for

Re: [gmx-users] Analysis using sh file

Hi, On Tue, Feb 4, 2020 at 11:14 AM wrote: > 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 trying to use a .sh, as I was > > doing in the version 5.0.4, now I'm receiving back an error since the > > syntax

Re: [gmx-users] Selecting water molecules within a nanotube

Hi, On Tue, Feb 4, 2020 at 9:19 AM RAHUL SURESH wrote: > Hi Users. > > I am simulating a nanotube in water medium. The nanotube is aligned to the > center of the box using gmx editconfig and solvate. But I want to remove > the water molecules within the nanotube. How do I compute this ? > > I

Re: [gmx-users] how to generate tng format trajectory?

Hi, On Mon, Feb 3, 2020 at 4:39 PM Albert wrote: > Hello all, > > I just learned that the tng trajectory format file is even more smaller > than the .xtc format file. I am just wondering how shall we specify the > option in the .mdp file so that "gmx mdrun" could generate the .tng > format

Re: [gmx-users] How to use TIP4P-ICE water model

Hi, I did not fully understand what you have done. But my suggestion will be to use the pre-build tip4p.gro to build the water box and then perform the simulation with the topology of tip4p-ice and run long enough to allow the molecular system to relax, then check RDF. If the profile is not what

Re: [gmx-users] TraPPE-EH in GROMACS

Hi Maybe the definitions in the manual page (middle part) below may help you. ( http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html?highlight=file%20top ) Best regards Alessandra On Tue, Jan 28, 2020 at 8:41 AM Dhrubajyoti Maji wrote: > Dear

Re: [gmx-users] gmx distance error - invalid index with -f vs -s input file

Hi, see below On Thu, Jan 23, 2020 at 7:34 PM Travis Meyer wrote: > Hello all, > > I am using gmx distance to extract bond distances from a set of 200 > coarse-grained polymer molecules (10 "atoms" each). I created an index file > pointing to all of the bonds, and ran the command as > > gmx

Re: [gmx-users] Calculation of an energy term for stretching

Hi, Below some suggestions On Thu, Jan 23, 2020 at 3:52 PM wrote: > Dear collegues, > > I am trying to write an energy function for my molecule that will imitate > the results of the amber energy function. For this reason, I calculated > all energy terms for my molecule (printed all terms for

Re: [gmx-users] MD simulation stops without any error/warning message

Hi, On Thu, Jan 23, 2020 at 2:04 PM Michele Pellegrino wrote: > Hi, > > > today I was running a MD simulation and it stopped without any > error/warning message. > > It just stopped: the md.log file reported everything till the last time > step, and no information on the nature of the

Re: [gmx-users] How to set the temperatures for REMD?

Hi, On Wed, Jan 22, 2020 at 5:55 PM ZHANG Cheng <272699...@qq.com> wrote: > My purpose of running REMD is to generate sufficient conformation > sampling, and try to use them to explain the in vitro data at 65C (338.15K). > > > I am using the "Temperature generator for REMD-simulations" at >

Re: [gmx-users] Assertion failed for the REMD tutorial

Hi, On Tue, Jan 21, 2020 at 9:55 PM ZHANG Cheng <272699...@qq.com> wrote: > I am trying to follow the REMD from Mark Abraham at > >

Re: [gmx-users] compressibility values in coarse grained simulations

Hi, On Fri, Jan 3, 2020 at 12:04 PM Deepanshi . wrote: > Dear all, > > I am using the coarse-grained molecular dynamics simulation to study > membranes. In the production run .mdp file, to control the pressure I am > using semiisotropic in the Pcoupltype option. I wanted to ask how many >

Re: [gmx-users] Uniaxial elongation using deform option

Hi, Some comments below. I hope they help you On Mon, Jan 20, 2020 at 6:51 AM Pragati Sharma wrote: > Dear all, > > I want to calculate young's modulus of a polymer using uniaxial elongation. > (elongation in z axis but no volume change) > I am using 'deform' option and semiisotropic pressure

Re: [gmx-users] Problem while running equilibration

Hi, see some comments/suggestions below. Best regards Alessandra On Fri, Jan 17, 2020 at 8:34 AM Nirali Desai wrote: > Dear all, > > My system consists of a three chains of protein: PROA, PROB and PROCLIG > (with ligand). > Minimization is running properly without any error. > Parameters used

Re: [gmx-users] Regarding high RMSD

Hi, On Fri, Jan 17, 2020 at 6:39 AM Ashma Khan wrote: > Thank you for your suggestion Alessandra Villa > I have applied all types of pbc conditions but my one peptide is diffusing > away from another peptide in case of dimer after half of the simulation > time and rmsd is co

Re: [gmx-users] A list of missing interactions

Hi, my suggestion is to follow the indication that you got from the error See the mdrun " option -rdd, for pairs and tabulated bonds also see option -ddcheck" Best regards Alessandra On Wed, Jan 15, 2020 at 12:33 AM Sadaf Rani wrote: > Dear Gromacs users > I am facing this error during free

Re: [gmx-users] com motion and position restraints may cause artifacts

Hi, On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris wrote: > dear all, > > I installed gromacs 2020 and I now get the following message during > equilibration: > > NOTE 1 [file nvt.mdp]: > > Removing center of mass motion in the presence of position > restraints might cause artifacts > >

Re: [gmx-users] Troubleshooting Error Message: Invalid Index Group References

Hi, On Tue, Jan 14, 2020 at 7:41 PM Travis Meyer wrote: > Hello all, > > I am a brand new MD/GROMACS user, and I have been trying to learn how to > use GROMACS for coarse-grained simulations using the MARTINI forcefield. I > was going through a tutorial on coarse-graining from the MARTINI

Re: [gmx-users] Regarding high RMSD

Hi, I suggest to visualize your trajectory. Maybe one of the peptide is diffusing away from the other. Or the one peptide is jumping in and out or moving out the box. If it is the case, here you found some trjconv workflow

Re: [gmx-users] cut-off scheme

Hi, my suggestion is to move to Verlet scheme - (http://manual.gromacs.org/documentation/2019/user-guide/cutoff-schemes.html ) See also for http://manual.gromacs.org/documentation/2020/release-notes/2019/major/deprecated-functionality.html#functionality-deprecated-in-gromacs-2019 You could

Re: [gmx-users] gmx genconf

Hi, gmx genconf is not generating xtc files. -trj option allows to use the trj frames to expand gro/pdb files. For example using -nbox 2 2 2 the first 8 frames of the trj file will be use to build the new gro/pdb file. A possible alternative is to use If you want to visualize you xtc-file

Re: [gmx-users] Loading topology into vmd

Hi, One of the criteria that VMD uses to define bond is distance criteria. When you source your gro file, this criteria is applied. One way one, I have used is to not visualize undesired bonds, is the following: delete the undesired bonds, save the vmd setting (*.vmd file), load the setting

Re: [gmx-users] Cut off (1.2 -1.5 nm) with OPLS forcefield

Hi, A general criteria is to apply the short and long range interaction setting used in the parametization procedure. Each force field has its own parameterization strategy. Among other that guarantees parameters consistency and results reproducibility. Another story is if you are performing your

Re: [gmx-users] Query regarding do_dssp program

Hi, VMD and dssp may use a slightly different criteria to define a beta sheet. First I will check in literature if the criteria are the same. In some case, it occur that the the atom types (e.i H) are not properly recognized by the software, and thus secondary structure element can not be

Re: [gmx-users] gmx_topolbuild error

Hi, I am not familiar with the software "topolbuild" (gmx topolbuild does not exist), but I have noticed that you are not using TRIPOS atom types in your mol2 file. Maybe that is a problem. Best regards Alessandra On Fri, Jan 10, 2020 at 7:03 AM wrote: > I am getting error in topolbuild: >

Re: [gmx-users] Position restrains calculation of virial

Hi Johannes, On Wed, Jan 8, 2020 at 11:29 AM Johannes Hermann wrote: > Dear all, > > how is the virial computed when position restraints are applied? Are > forces due to position restrains included or excluded? > > Yes the the forces due to position restrains are included. But I think that

Re: [gmx-users] Make index command in gromacs

Hi, Maybe you could use gmx select to generate your index file http://manual.gromacs.org/documentation/current/onlinehelp/gmx-select.html?highlight=select Best regards Alessandra On Tue, Jan 7, 2020 at 11:39 PM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > Dear Gromacs Users, > >

Re: [gmx-users] segmantation fault

Hi, Maybe the nvt.log file provides you more information on the problem Best regards Alessandra On Fri, Dec 20, 2019 at 9:40 AM Bratin Kumar Das < 177cy500.bra...@nitk.edu.in> wrote: > Dear all, > During running nvt equilibration I got the following error. > gmx mdrun -v -s

Re: [gmx-users] constraints

Hi On Thu, Dec 19, 2019 at 3:41 PM Maria Luisa wrote: > Dear users, > I want to constraints a group of molecules inside a tri-layer structure. > How can I label and fix these molecules ? > > Depends on the problems, but to fix atoms to a reference position, you can use position restraints (

Re: [gmx-users] LINCS constraint on DU-DU bond

Hi, On Fri, Dec 13, 2019 at 1:53 PM Luirink, R.A. wrote: > Hi, > I would like to constrain a bond between two dummy atoms using LINCS > constraints. As I want to perturb the atoms towards a N-H bond, I would > like to pre-treat it as such, due to the low mass of one of the dummy atoms. > Is

Re: [gmx-users] Selecting multiple dihedral angles with common atoms

Hi, On Sat, Dec 14, 2019 at 4:12 AM Pathum Manjula Weerawarna < pathum.weerawa...@northwestern.edu> wrote: > Hi, > > > Is there anyway to select multiple dihedral angles with common atoms in > gmx angle to prepare a trr file for dihedral PCA analysis? I can select > multiple dihedral angles when

Re: [gmx-users] Small molecule with transition metal (Fe)

Hi, On Mon, Dec 16, 2019 at 10:22 PM Venoos Amiri Roodan wrote: > Hi, > > I am trying to do molecular dynamic analysis for the combination of small > molecule with Fe, Heme with Fe and eventually do YbtFe(III). I am having > difficulties assigning the right forcefield for the iron atom. > >

Re: [gmx-users] setting distance restraints between atoms belonging to different residues (Alessandra Villa)

Hi, I meant to use the option of "-merge" of pdb2gmx, to generate one file for protein + ligands (top) Best regards Alessandra On Fri, Dec 13, 2019 at 11:44 AM Sadaf Rani wrote: > Thank you, Alessandra, for your reply. > > I have a confusion here that when I merge the topology I will have to >

Re: [gmx-users] question regarding gmx helix orientation

Hi, On Thu, Dec 12, 2019 at 1:09 PM SHAHEE ISLAM wrote: > hi, > i want to calculate the tilt angle of helix against the bilayer normal. > First i made a index file which contains the backbone of the residues of > large helix. I am using this command > *gmx helixorient -s *.tpr -f *.xtc -n

Re: [gmx-users] Add new window for MBAR calculation

Hi, Just a suggestion. On Wed, Dec 11, 2019 at 7:17 AM Александр Лашков wrote: > Dear colleagues. I use the MBAR algorithm to process the results of an > alchemical conversion in GROMACS. If I find a bad states overlaps, is it > possible to add a new window without fully recomputind MD

Re: [gmx-users] How to calculate potential energy with dynamics selection index?

Hi On Fri, Dec 6, 2019 at 5:36 AM Peiyin Lee wrote: > Dear users, > >I am trying to calculate the VDW potential energy and electrostatic > energy for solvent in the first solvation shell and in bulk for my > simulation systems. In order to calculate the potential for solvent in the > FSS, I

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

Hi, Maybe trjconv workflow below can help you to visualize your droplet (without no com motion) http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=trjconv Best regards Alessandra On Thu, Dec 5, 2019 at 9:49 PM Alex wrote: > Hi all, > > I have a droplet

Re: [gmx-users] Check the 1-4 interactions, and the non-bonded pairs in the output

Hi On Thu, Dec 5, 2019 at 7:01 PM Suvardhan Jonnalagadda < j.su.vard...@gmail.com> wrote: > Hi all, > > I have performed NPT simulation in GROMACS 5.4.1. In the 'forcefield.itp' > file I have mentioned 'gen-pairs' as 'yes', and also the 'Fudge-LJ' was > specified. From the output I want to check

Re: [gmx-users] Potential or total energy in dhdl files

le. Best regards Alessandra > Alexander > > ср, 4 дек. 2019 г. в 12:02, Alessandra Villa < > alessandra.villa.bio...@gmail.com>: > > > HI, > > > > On Tue, Dec 3, 2019 at 3:56 PM Александр Лашков > > wrote: > > > > > Dear gromacs te

Re: [gmx-users] Potential or total energy in dhdl files

HI, On Tue, Dec 3, 2019 at 3:56 PM Александр Лашков wrote: > Dear gromacs team, you wrote in documentation "This information is needed > for later free energy analysis if the states of interest are at different > temperatures. If all states are at the same temperature, this information > is not

Re: [gmx-users] Overriding atom type.

Hi, On Wed, Dec 4, 2019 at 7:41 AM Yogesh Sharma wrote: > Hello Users, > I was trying to run grompp for a membrane protein - ligand dynamics. I am > using 4 5 ligands together. Under grompp run I got error overriding > atomtype HGP1. Came out two ligands were sharing similar naming in

Re: [gmx-users] Two atom oscillational period less than the time step

Hi, On Tue, Dec 3, 2019 at 7:37 AM Mijiddorj B wrote: > Dear GMX users, > Hello, I would like to discuss the grompp message that tells the bonded > atoms oscillational period less than 10 times the time step. I am using > 0.002 ps time step. The choice of the time step depends on the force

Re: [gmx-users] Disulphide bonded cyclic peptides

ls_X > atomtypes? > > In the entries of the forcefied file *.rtp, *n.tdb and in *c.tdb. Best regards Alessandra > Best regards, > > Sahil > > On 2019-11-29 15:46, Alessandra Villa wrote: > > > Hi, > > > > On Fri, Nov 29, 2019 at 8:30 AM Sahil Lall wrote: &

Re: [gmx-users] Disulphide bonded cyclic peptides

ing termini. > Now there are 6 residues with 96 atoms > Making bonds... > Number of bonds was 99, now 98 > Generating angles, dihedrals and pairs... > Before cleaning: 258 pairs > Before cleaning: 258 dihedrals > Keeping all generated dihedrals > Making cmap torsions...There are

Re: [gmx-users] Calculation of young's modulus from stress-strain plot

Hi, On Thu, Nov 28, 2019 at 1:23 PM Pragati Sharma wrote: > Hello users, > > I am trying to plot stress-strain curve for natural rubber from NPT > simulations using the "deform" option. Deform along x direction at 1 bar > pressure. The parameters I gave in mdp file are: > > Pcoupl

Re: [gmx-users] Disulphide bonded cyclic peptides

Hi again, On Thu, Nov 28, 2019 at 11:06 AM Sahil Lall wrote: > Hello, > > I am extremely thankful for your suggestions, but I have a few concerns > with your advice as stated below. > > > Hi, > > Below some suggestion that may help you. > > > > On Wed, Nov 27, 2019 at 7:44 AM Sahil Lall wrote:

Re: [gmx-users] Terminal dangling bond error despite pdb2gmx recognising specbond.dat for a cyclic peptide

Hi, I have just answered to your previous email. Please look at my answer. Thank you Alessandra On Thu, Nov 28, 2019 at 9:41 AM Sahil Lall wrote: > Dear community, > > I want to use the OPLS-AA ff to understand the dynamics of a cyclic > peptide with terminal-peptide-bonded Cystines that are

Re: [gmx-users] Disulphide bonded cyclic peptides

Hi, Below some suggestion that may help you. On Wed, Nov 27, 2019 at 7:44 AM Sahil Lall wrote: > Dear community, > > I want to use the OPLS-AA ff to understand the dynamics of a cyclic > peptide with terminal Cystines that are disulphide linked. To cyclise > the N- and C- termini, I used a

Re: [gmx-users] Dummy atoms flopping everywhere

calculations.html Best regards Alessandra > Best > > Le mer. 27 nov. 2019 à 03:26, Alessandra Villa < > alessandra.villa.bio...@gmail.com> a écrit : > > > Hi, > > > > On Mon, Nov 25, 2019 at 6:20 PM Raphaël Robidas < > raphaelrobi...@gmail.com>

Re: [gmx-users] Dummy atoms flopping everywhere

Hi, On Mon, Nov 25, 2019 at 6:20 PM Raphaël Robidas wrote: > I am doing a free energy perturbation calculation on a protein-ligand > system. I am going from a topology A which has a benzyloxy group to a > topology B which only has a methoxy group. My problem is that when lambda = > 1, the

Re: [gmx-users] Regarding free energy calculation

Hi, You could try AMBER99 BSC1. FF implementation could be found in http://www.gromacs.org/Downloads_of_outdated_releases/User_contributions/Force_fields (amber99bsc1.ff.tgz ) Best regards Alessandra

Re: [gmx-users] How does the trjconv -fit rot+trans work?

Hi, On Wed, Nov 27, 2019 at 7:12 AM Nirali Desai wrote: > Dear all, > > I want to understand the use of trjconv for shifting a protein system to > reference structure. > I am able to understand the coordinates would be translated by -trans , but > how does gromacs take care of rotation of the

Re: [gmx-users] Chain length of a polymer

Hi, I understood, that you would like to monitor the distance between the two ends of your chains along the simulation. If this is the case you could use gmx distance (see http://manual.gromacs.org/current/onlinehelp/gmx-distance.html) together with the appropriate selection (e.i. you could

Re: [gmx-users] (no subject)

Hi, Pls note that the maillist does not support attachments. Also it will better/helpful to use emails subject. Kind regards Alessandra On Tue, Nov 19, 2019 at 10:46 AM pooja kesari wrote: > Dear All, > I am doing a protein-ligand simulation, when i was try to *add ions to the > system* > gmx

Re: [gmx-users] helping increasing box

Hi, What you see, is the effect of boundary condition.To avoid this visualization effect, before increasing the box, you may want to check that your system is whole and better center in the gro file. Best regards Alessandra . On Thu, Nov 14, 2019 at 10:28 PM Giuseppe R Del Sorbo wrote: >

Re: [gmx-users] Question about switching off non-bonded interactions between two molecules for MD simulation

Hi, As far as I understood, you have a protein and ligand (not covalently bonded) and you want to switch off the interaction between one aminoacid and the ligand. Concerning approach 1, If you have a merged topology (only one topology file with one [molecular type] in your case protein and

Re: [gmx-users] How to produce "gro" format for calcite {1014} structure.

Hi, Maybe you could try to convert the cif format to pdb format, if you feel that your conversion from cif to gro format is not working. Best regards Alessandra On Tue, Nov 12, 2019 at 5:09 PM Hamid Zaree wrote: > Hi. > I would like to simulate Calcite structure in GROMACS. How could I make the