Re: [gmx-users] using enegygrps

Hi Dr.Lemkul Thank you very much for your answer and your time I m using Gromos 54a7 force field, How can I find my force field is parametrized in such a way that the nonbonded energy decomposition has some physical meaning? Thank you Regards Azadeh -- This email was Anti Virus checked

Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs

On 2/14/18 5:28 PM, Easton J.W. wrote: Hi Justin, Many thanks for the detailed reply. I just wanted to check that it doesn't matter that the A2C and A3C are not present in the bonded and non-bonded itp files for the forcefield? Should this not have given an error? The topology snippet

Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs

Hi Justin, Many thanks for the detailed reply. I just wanted to check that it doesn't matter that the A2C and A3C are not present in the bonded and non-bonded itp files for the forcefield? Should this not have given an error? Kind regards, James From:

Re: [gmx-users] Flexible and posres

On 2/14/18 2:47 PM, Iman Ahmadabadi wrote: Dear Justin, Because there is a movement on atoms that posres should act on them, and this condition doesn't occur when the flexible option is not used. Restraints don't prevent movement, only disfavor it. Have you quantified this in any way?

Re: [gmx-users] Flexible and posres

Dear Justin, Because there is a movement on atoms that posres should act on them, and this condition doesn't occur when the flexible option is not used. Sincerely, Iman On Wed, Feb 14, 2018 at 8:48 PM, Iman Ahmadabadi wrote: > Dear Mark, > > I forgot the D in

Re: [gmx-users] using enegygrps

On 2/14/18 1:15 PM, kordza...@aut.ac.ir wrote: Hi all I want to investigate interaction drug and bilayer for more detailed investigation I want to use energygrps for functional group of drug to find out which part of drug has more interaction. is energygrps good tool? If the force field

Re: [gmx-users] pressure coupling error in umbrella sampling

On 2/14/18 1:06 PM, kordza...@aut.ac.ir wrote: Hi Dr.Lemkul Thank you very much for your answer I get it now, before your answer I run system with -maxwarn 1, I saw trajectory in vmd , my drug molecule break in middle of run and then corrected, is it wrong? No, that's called periodic

[gmx-users] using enegygrps

Hi all I want to investigate interaction drug and bilayer for more detailed investigation I want to use energygrps for functional group of drug to find out which part of drug has more interaction. is energygrps good tool? Thank you very much Regards Azadeh -- This email was Anti Virus

Re: [gmx-users] pressure coupling error in umbrella sampling

Hi Dr.Lemkul Thank you very much for your answer I get it now, before your answer I run system with -maxwarn 1, I saw trajectory in vmd , my drug molecule break in middle of run and then corrected, is it wrong? has it occured because using maxwran? is vmd an appropriate tool for detect

Re: [gmx-users] Flexible and posres

On 2/14/18 12:18 PM, Iman Ahmadabadi wrote: Dear Mark, I forgot the D in -DPOSRES in the previous email. However I used the "define = -DFLEXIBLE -DPOSRES" but it doesn't work and position restraint was not applied on the atoms. Is there another way to solve the problem? What proof can you

Re: [gmx-users] Flexible and posres

Dear Mark, I forgot the D in -DPOSRES in the previous email. However I used the "define = -DFLEXIBLE -DPOSRES" but it doesn't work and position restraint was not applied on the atoms. Is there another way to solve the problem? Respectfully, Iman On Wed, Feb 14, 2018 at 5:48 PM, Iman Ahmadabadi

Re: [gmx-users] Calculation of shape change of a protein during simulation

Dear Joao and Thomas, Thanks a lot for your kind reply. I am able to calculate the desired properties by following your answer. Best regards, Sudip ‌ Sudip Das PhD Student C/o. Prof. S. Balasubramanian Molecular Simulations Lab Chemistry and Physics of Materials Unit (CPMU) Jawaharlal Nehru

Re: [gmx-users] Calculation of shape change of a protein during simulation

You can calculate properties describing molecular shape using PLUMED as a trajectory post-processing tool. Example input: GROUP ATOMS=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47 LABEL=al GYRATION TYPE=RADIUS

Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs

On 2/14/18 9:42 AM, Justin Lemkul wrote: On 2/14/18 9:33 AM, Easton J.W. wrote: Thanks Justin, Will this effect the interactions (both bonded and non-bonded) that these atoms have, as their atom types are not in the forcefield itp files? Missing atom types would cause grompp to fail;

Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs

On 2/14/18 9:33 AM, Easton J.W. wrote: Thanks Justin, Will this effect the interactions (both bonded and non-bonded) that these atoms have, as their atom types are not in the forcefield itp files? Missing atom types would cause grompp to fail; you'd never get to the point where a

Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs

Thanks Justin, Will this effect the interactions (both bonded and non-bonded) that these atoms have, as their atom types are not in the forcefield itp files? Kind regards, James From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs

On 2/14/18 7:14 AM, Easton J.W. wrote: Hi, I've used acpype to convert my prmtop and inpcrd files into gromacs format. I'm using the amber14sb forcefield. At the top of the top file generated, is an [atomtypes] section. Most of the atoms in this section were present in the atomtypes.atp

Re: [gmx-users] Rupture force definition

On 2/14/18 7:31 AM, Rakesh Mishra wrote: Dear Justin, Can you explain something regarding this issue. I couldn't get resolve one problem. Though now I am able to make restrict (immobile ) the needed residue and pulled another one. But the contradiction that i am facing is that, when I am

Re: [gmx-users] Flexible and posres

Hi, Please copy and paste your attempts and the errors, if you want to get effectively help. You can use define = -DPOSRES -DFLEXIBLE to combine them, and -POSRES is always wrong. Mark On Wed, Feb 14, 2018 at 3:19 PM Iman Ahmadabadi wrote: > Dear Gromacs Users, >

Re: [gmx-users] the energy of the individual molecule

On 2/13/18 11:48 AM, dgfd dgdfg wrote: Suppose the trajectory of molecular system with interactions between all molecules. How is to obtain the time dependence of intramolecular energy of the given molecule with unique resname and the total energy of this molecule in the system including

[gmx-users] Flexible and posres

Dear Gromacs Users, If I wanna use some flexible bonds and also use position restraint on some other atoms, how should I do this? the error arises because 2 define = -DFLEXIBLE and -POSRES is not allowed in the .mdp files. Respectfully -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] Pulling protein from distance on membrane

On 2/13/18 5:24 AM, Souparno Adhikary wrote: Hi, I am trying to simulate a system in which a protein will be pulled from a distance and ultimately be put on a DPPC membrane system. I went through Lemkul's tutorial on membrane and successfully simulated protein-membrane systems before. In

Re: [gmx-users] GROMOS96 53A6 with extended Berger lipid parameters (Prasanna)

On 2/13/18 5:08 AM, Prasanna Dr wrote: Hi all, The force field combination used in GROMOS96 53A6 with extended Berger lipids contains L-J interaction cross-terms between protein lipid atom types? If so how abnormally high L-J interactions are tackled? In my case, to prepare the topology of

Re: [gmx-users] charmm36 force field

On 2/12/18 3:09 PM, farial tavakoli wrote: First, please note that this line is not doing anything: define        =  -DUSE_OLD_C3 If you're trying to use the old CHARMM36 parameters, and not CHARMM36m, the correct keyword is -DUSE_OLD_C36. We only included that in the case that people

Re: [gmx-users] how can i restrain Zn ion during simulations

On 2/12/18 10:29 AM, vijayakumar gosu wrote: Dear gromacs users, I am currently running simulations for protein-RNA complex. However i have to include one Zn ion which is coordinated by 4 cysteine residues. when i performed energy minimization itself zinc displaces. How can i restrain to Zn,

Re: [gmx-users] PBC

On 2/12/18 8:44 AM, Ahmed Mashaly wrote: Hi If I want to use gmx trjconv to recenter the protein in xtc file, the reference (-s) .tpr should be the one I used in simulation (md.tpr) or I can use the first one (em.tpr) without a difference? This is because the protein has jumped after em

Re: [gmx-users] pressure coupling error in umbrella sampling

On 2/12/18 6:34 AM, kordza...@aut.ac.ir wrote: Hi Dr.Abraham Thank you very much for your answer yas I ve extacted configuration with 0.2 nm distance and when I want to run NPT for first configuration,I gave that error. I didnt undersatnd this mdp file for this step, I got this file from

Re: [gmx-users] Rupture force definition

Dear Justin, Can you explain something regarding this issue. I couldn't get resolve one problem. Though now I am able to make restrict (immobile ) the needed residue and pulled another one. But the contradiction that i am facing is that, when I am pulling with -rate (in negative z direction,

[gmx-users] Potential issue using acpype to convert amber topology to gromacs

Hi, I've used acpype to convert my prmtop and inpcrd files into gromacs format. I'm using the amber14sb forcefield. At the top of the top file generated, is an [atomtypes] section. Most of the atoms in this section were present in the atomtypes.atp and ffnonbonded.itp so I deleted them

[gmx-users] printing neighbor list

Hi, I am trying to output the neighbor list calculated during a simulation. I consulted the manual which says that DUMPNL is the env variable suited for this purpose. In my bash script I first set up: export DUMPNL=10 and then run the simulation (GROMACS version 4.5.4). I do not see any