Re: [gmx-users] generating martini-version of lipids

Hi Tsjerk Thanks for your response. I was mainly looking for converting a dppg bilayer in charm36 format into a coarse-grained one. However, the "Mapping" folder does not have any mapping for dppg lipids. Is there any specific suggestion regarding this? Jagannath On Mon, Feb 29, 2016 at 10:10 PM

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

Thanks Peter, I thought as much. At the time it just seemed like an odd bit of information to report. Many thanks Anthony Dr Anthony Nash Department of Chemistry University College London On 01/03/2016 03:15, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Peter Stern" wrot

[gmx-users] Deuterium order parameter for POPC/POPS mixed lipid bilayer

Hello everyone, I want to calculate deuterium order parameter for 25POPC/103POPS mixed lipid bilayer. But, I don't know how to make index groups for sn1 and sn2 acyl chains for both POPS and POPC lipids separately. Please help. Regards Kamakshi -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Sulfate ion parameters

Dear Mark, Thanks for the reply. Actually, I emailed the corresponding author but didn't get any reply. Also, it is not mentioned in the paper that the model is for a rigid system. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technologi

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

This is a non-problem. You will never get zero eigenvalues for such a large system since you are not at an absolute minimum. The fact that you got no negative eigenvalues and the six lowest eigenvalues are very small (surely much, much smaller than the subsequent eigenvalues) indicates that yo

Re: [gmx-users] creating representative structures

Dear all, I was able to write a tcl script to do cluster analysis, here I am using the gromos method. However, my script is giving slightly different results! I am testing my script on a smaller trajectory (8 frames). In the gromos method, the structure with the greatest number of neighbors is con

Re: [gmx-users] Calculate energy associated with hydrogen bond

Hi, This paper might be helpful https://www.researchgate.net/publication/222873041_Hydrogen_bond_strengths_revealed_by_topological_analyses_of_experimentally_observed_electron_densities_Chem_Phys_Lett. But you would need to know which is donor and acceptor, and which hydrogen. But that you can

Re: [gmx-users] Coarse grain membrane simulation of DPPC

Hi Ali, Coarse grain and atomistic system probably respond differently to high pressures. Cheers, Tsjerk On Feb 29, 2016 21:23, wrote: > > > > > Dear all > > > Recently I saw an article about 128DPPC of lipid bilayer. it > says that the bilayer would rupture by a > lateral 20

[gmx-users] No bonds in *.top file

Dear Gromacs Experts, I run gmx pdb2gmx and it runs without any warnings or errors by the *.top file does not contain any bonds. The *.gro file is fine and all hydrogen atoms are added correctly. Now I have discovered that when I get rid of calcium ions in my *.pdb file I get proper *.top file. B

[gmx-users] Coarse grain membrane simulation of DPPC

Dear all Recently I saw� an article about 128DPPC� of lipid bilayer. it says that the bilayer would rupture by a lateral 200bar tension, using Gromacs all atom. now I want to gain that using coarsegrain method. for all atom the pdb file is obtainable but for CG, I built it us

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

Hi all, Hoping this will be the final stumbling block. I’ve successfully minimised my structure to a a very small max force: Potential Energy = -1.93736854460113e+03 Maximum force = 7.39399083846082e-04 on atom 34 Norm of force = 1.64068483698544e-04 When I perform integrator=nm there

Re: [gmx-users] magnetic field

Magnetic field and electric are not same.also, they have not same effect. my molecule is asphaltene. Thanks for your answer On Monday, February 29, 2016, Kowsar Khajeh wrote: > Hello. > My question is that; > Does it possible to apply an external field ( like magnetic field ) to the polar molecul

Re: [gmx-users] nrexcl

Hi, I expect that there isn't a maximum. But IIRC grompp tells you what it is doing with exclusions, and the output of gmx dump -s your.tpr is definitive. Mark On Mon, Feb 29, 2016 at 8:24 PM Parvez Mh wrote: > Dear all, > > I would like to know what is the maximum *nrexcl* allowed in gromacs

[gmx-users] nrexcl

Dear all, I would like to know what is the maximum *nrexcl* allowed in gromacs. Regards Masrul -- 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_Li

[gmx-users] Calculate energy associated with hydrogen bond

Hi Everyone, Can anyone let me know how to calculate energy associated with hydrogen bond? Particularly if I am not sure which one is the acceptor (or donor) or there is a probability of more than one acceptor for a given donor or vice versa. Thanks a lot. "A society with free knowledge is better

[gmx-users] Box size for decoupled molecule in NpT ensemble

Dear Gromacs-users, I've a question regarding Gibbs free energy simulations. As the volume can fluctuate in the NpT-ensemble and is an extensive quantity, I do expect an intrinsic volume for the decoupled solute in the gas phase. Is there any chance to display this value? Regards, Andreas -

Re: [gmx-users] generating martini-version of lipids

Hi Jagannath, Backward actually can do both. For conversion of a Gromos system use backward.py -from gromos -to martini Hope it helps, Tsjerk On Mon, Feb 29, 2016 at 11:20 AM, Jagannath Mondal wrote: > Dear Gromacs/Martini-users > > I wanted to transform a snapshot of my atomistic DPPG/wate

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

Dear Mark and Justin, By removing the restraints (your suggestions) it appears to have worked! Maximum force: 9.21098e-04 Writing Hessian... This now matches the same force as my energy minimisation. Many thanks for you help. Thanks Anthony Dr Anthony Nash Department of Chemistry University

[gmx-users] Note of geometric combination rules in LJ-PME

Dear GmxUsers, Recently I got this Note in my enegy minimization (l-bfgs) step. I am using 5.1.1 version.    You are using geometric combination rules in LJ-PME, but your non-bonded  C6 parameters do not follow these rules. This will introduce very small  errors in the forces and energies in

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

Hi, An earlier mdp file suggested you were using position restraints. There should be no need for this, nor any problem, but what happens without them? Mark On Mon, 29 Feb 2016 15:39 Nash, Anthony wrote: > Hi Justin, > > After some digging I had found that link and made some adjustments (as >

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

Hi Justin, After some digging I had found that link and made some adjustments (as presented in the later email). After a series of energy minimisations (including switching LINCS off, and dropping the energy step to a very small number), and with the final command: grompp_d -f cg.mdp -c modic_cg_

[gmx-users] Note of geometric combination rules in LJ-PME

Dear GmxUsers, Recently I got this Note in my enegy minimization (l-bfgs) step. I am using 5.1.1 version.    You are using geometric combination rules in LJ-PME, but your non-bonded  C6 parameters do not follow these rules. This will introduce very small  errors in the forces and energies in you

Re: [gmx-users] Acpype topolgy error

On 2/29/16 7:56 AM, Mutemi Chief wrote: Just change ca to C ie carbon. Pay attention to the atomic masses indicated I would strongly advise against doing this, unless it is 100% certain that C and ca have equivalent bonded and nonbonded parameters. The acpype topology should include all n

Re: [gmx-users] Acpype topolgy error

Just change ca to C ie carbon. Pay attention to the atomic masses indicated -Original Message- From: "Justin Lemkul" Sent: ‎29/‎02/‎2016 15:50 To: "gmx-us...@gromacs.org" ; "Abid Channa" Subject: Re: [gmx-users] Acpype topolgy error On 2/29/16 4:51 AM, Abid Channa wrote: > Dear Grom

Re: [gmx-users] [gmx-developers] how to deal with improper dihedral angles

On 2/29/16 3:29 AM, Javaria ashraf wrote: hello and good day sir i have query related to improper dihedral angles my topol.top file shows 1082 improper dihedral angles, I have used opls-forcefield, and no water model sample: 1801 1806 1802 1803 1improper_Z_CA_X_Y 1801 1808 1804

Re: [gmx-users] protein-DNA complex

On 2/29/16 4:25 AM, Mahboobeh Eslami wrote: dear Justin thanks for your answer I have another question. Which of the following items is better in mdp file for the equilibration and MD production steps? tc-grps = Protein-DNASOL-ION or tc-grps = Protein DNA SOL-ION Probab

Re: [gmx-users] Acpype topolgy error

On 2/29/16 4:51 AM, Abid Channa wrote: Dear Gromacs users, I am going to run complex simulation. I have prepared ligand topology through acpype , from where I have taken two files .gro and .itp file. I have used Gromos ff for my simulation . I got atom type error while running this command "

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

On 2/29/16 3:41 AM, Nash, Anthony wrote: Hi Tsjerk, The two .mdp files are virtually identical (the only exception being what defines one as a conjugate-gradient, and the other for normal mode analysis): CONJUGATE GRADIENT: define = -DPOSRES integrator = cg emtol = 0.001 emstep

Re: [gmx-users] Coarse Grain using martinize.py

Dear Tsjerk I had a similar question. I guess insane.py script is supposed to build a coarse-grained membrane/solvent system from scratch. But, if I already have a particular existing atomistic configuration of lipid/water system along with some proteins ( which I had obtained by performing an at

Re: [gmx-users] Sulfate ion parameters

Hi, Such questions are why all published articles list the email address of a "corresponding author" ;-) But first, be sure their model wasn't designed to be rigid, and so have no internal parameters such as you are seeking. Mark On Mon, Feb 29, 2016 at 12:01 PM #SUKRITI GUPTA# wrote: > Thanks

[gmx-users] Fw: protein-DNA complex

On Monday, February 29, 2016 12:55 PM, Mahboobeh Eslami wrote: dear Justinthanks for your answerI have another question. Which of the following items is better in mdp file for the equilibration and MD production steps? tc-grps   = Protein-DNASOL-ION or tc-grps   = Protein

Re: [gmx-users] magnetic field

Hi, On Mon, Feb 29, 2016 at 10:56 AM Kowsar Khajeh wrote: > Hello. > My question is that; > Does it possible to apply an external field ( like magnetic field ) to the > polar molecules in the simulation box in gromacs? Yes, there's a (very small) part in the reference manual about applying an

Re: [gmx-users] Sulfate ion parameters

Thanks for the reply. I got one paper stating non bonded parameter values for sulphate ions: "Sulfate Anion in Water: Model Structural, Thermodynamic, and Dynamic Properties", but this paper does not provide bonded parameters required for simulating sulfate ions, i.e. bond bending and stretchi

Re: [gmx-users] Coarse Grain using martinize.py

Dear Tsjerk I had a similar question. I guess insane.py script is supposed to build a coarse-grained membrane/solvent system from scratch. But, if I already have a particular existing atomistic configuration of lipid/water system along with some proteins ( which I had obtained by performing an at

[gmx-users] generating martini-version of lipids

Dear Gromacs/Martini-users I wanted to transform a snapshot of my atomistic DPPG/water bilayer to the Martini coarse-grained format. However, I found martinize.py script does not transform lipid or waters to coarse-grained counterpart.It only works for protein. So, Is there any particular way I c

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

I noticed that I hadn’t included LINCS parameters in the mdp file. I have included and currently running using: continuation = no constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 2 ; accuracy of LINCS lincs_order

[gmx-users] magnetic field

Hello. My question is that; Does it possible to apply an external field ( like magnetic field ) to the polar molecules in the simulation box in gromacs? in fact, can we define polar molecules in the box? thanks Kosar Khajeh = PhD Candidate Faculty of Mechanical Engi

[gmx-users] Acpype topolgy error

Dear Gromacs users, I am going to run complex simulation. I have prepared ligand topology through acpype , from where I have taken two files .gro and .itp file. I have used Gromos ff for my simulation . I got atom type error while running this command  " gmx grompp -f em.mdp -c solv.gro -p topol

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

Hi Tsjerk, The two .mdp files are virtually identical (the only exception being what defines one as a conjugate-gradient, and the other for normal mode analysis): CONJUGATE GRADIENT: define = -DPOSRES integrator = cg emtol = 0.001 emstep = 0.0002 nsteps = 100

Re: [gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

Hi, The simplest explanation for this is that one set of runs used position restraints and one set did not. Mark On Mon, 29 Feb 2016 08:48 SAPNA BORAH wrote: > hi > Thanks for the suggestion. I will give this a shot, and remove these > restraints. > > I am unclear about what should I be lookin

[gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

On 29 February 2016 at 08:48, SAPNA BORAH wrote: > hi > Thanks for the suggestion. I will give this a shot, and remove these > restraints. > > I am unclear about what should I be looking in the log file as you > mentioned. The conformations are not just close, they are the same as the > initial c

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

Hi Anthony, You can paste your exact workflow commands and mdp files, but that would be to just check whether you overlooked something. If you assert that the mdp files are the same, except for the integrator and you really did use the final minimized structure as input for the nm run, then it see