[gmx-users] charge in *.n2t file

hi all I use from "charmm27.ff" force field for my work. below listed the parameter which i used in *.n2t file. how can find or calculate charge for each atoms (the third column) for charmm27 force field CCA??? 12.011 2C 0.142 C 0.142 CCA0.00 12.011 3C 0.

Re: [gmx-users] Charged group problem

Thank you Justin, as friendly as ever! Adriana *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..:+54 266 4424689 int

Re: [gmx-users] Question

On 8/12/15 5:12 PM, Eric Smoll wrote: Mark and Justin, Thank you for the help. It is much appreciated. Is there a way to prevent the output of an .edr file altogether? Is there a way to prevent the output of a .trr file all together? nstenergy = 0 nstxout = 0 nstvout = 0 nstfout = 0 Don't

Re: [gmx-users] Question

Mark and Justin, Thank you for the help. It is much appreciated. Is there a way to prevent the output of an .edr file altogether? Is there a way to prevent the output of a .trr file all together? Best, Eric On Wed, Aug 12, 2015 at 2:38 PM, Mark Abraham wrote: > Hi, > > On Wed, Aug 12, 2015 at

Re: [gmx-users] Change to umbrella sampling pull code

On 8/12/15 4:51 PM, Nash, Anthony wrote: Thanks for clearing that up Justin, I’ve adjusted accordingly. All but one error remains: Pull group 1 'ZINC' has 1 atoms Pull group 2 'CARBONYL' has 1 atoms --- Program grompp, VERSION 5.0.5 Source

Re: [gmx-users] Change to umbrella sampling pull code

Thanks for clearing that up Justin, I’ve adjusted accordingly. All but one error remains: Pull group 1 'ZINC' has 1 atoms Pull group 2 'CARBONYL' has 1 atoms --- Program grompp, VERSION 5.0.5 Source code file: /home/columbus/chem_software/GROM

Re: [gmx-users] Distance restrain with dummy atom

On 8/12/15 10:24 AM, anu chandra wrote: Dear Justin, Thanks for the reply. As you suggested I have tried with flat-bottomed position restraint. Unfortunately, the water molecules were seen to be moving to vacuum that leads to membrane distortion. The methodology I adopted is as follows, 1. I

Re: [gmx-users] Question

Hi, On Wed, Aug 12, 2015 at 9:47 PM Eric Smoll wrote: > Hello gromacs users, > > I am running a set of MD simulations where we are only interested in > logging the coordinates and kinetic energy of a specific group in the > system. I want to write the coordinates and energy of this group to file

Re: [gmx-users] Charged group problem

On 8/12/15 9:30 AM, Adriana Garro wrote: Dear users, My system contains peptide + TFE + water in an octahedron box. I am using oplsaa.ff I am trying to do EM but running this command grompp -f em.mdp -c C22_TFE-W.gro -p topol.top -o em.tpr the next error message come up WARNING 1 [file em.

Re: [gmx-users] Change to umbrella sampling pull code

On 8/12/15 3:20 PM, Nash, Anthony wrote: Hi Mark, Thanks for the reply. Comparing the documentation between manual-4.5.6 (what I had previously been using) and manual-5.0.4: 4.5.6 has reference to pull_group0 as reference group, and in 5.0.4 there is no explicit mention (that I can see) to a

Re: [gmx-users] Question

On 8/12/15 3:47 PM, Eric Smoll wrote: Hello gromacs users, I am running a set of MD simulations where we are only interested in logging the coordinates and kinetic energy of a specific group in the system. I want to write the coordinates and energy of this group to file at every timestep. Sup

Re: [gmx-users] Pdb file

Exactly. Gaseous LJ systems above a certain density will have a positive PE. Mark On Wed, Aug 12, 2015 at 9:23 PM sujithkakkat . wrote: > Hello, > > I guess it is not unusual for gaseous systems to have positive energy. I > hope that the Fmax criteria is satisfied. > > Sujith. > > On Wed, Aug

[gmx-users] Question

Hello gromacs users, I am running a set of MD simulations where we are only interested in logging the coordinates and kinetic energy of a specific group in the system. I want to write the coordinates and energy of this group to file at every timestep. Supplying an index file with the group of int

Re: [gmx-users] Pdb file

Hello, I guess it is not unusual for gaseous systems to have positive energy. I hope that the Fmax criteria is satisfied. Sujith. On Wed, Aug 12, 2015 at 10:30 AM, Sunil Ghimire wrote: > I mean potential energy of system (1600 argon atoms) is positive after > energy mininization . > On 12 Aug

Re: [gmx-users] bonded parameter

Hi, I mean that I can't possibly tell what your problem is, because you've shared zero information. You probably want to look at the PDF reference manual for the documentation of the "constraints" .mdp option. Whether that matters depends what you've chosen, but I don't know that. See http://www.g

Re: [gmx-users] Change to umbrella sampling pull code

Hi Mark, Thanks for the reply. Comparing the documentation between manual-4.5.6 (what I had previously been using) and manual-5.0.4: 4.5.6 has reference to pull_group0 as reference group, and in 5.0.4 there is no explicit mention (that I can see) to a reference group but there is one for the pul

Re: [gmx-users] bonded parameter

Yes, but only you know which! Mark ‪On Wed, Aug 12, 2015 at 8:45 PM ‫حسن هاشم زاده‬‎ < hashemzadehas...@gmail.com> wrote:‬ > this means that "bonded parameter" not necessary for my work or that my > work is wrong > > 2015-08-12 22:53 GMT+04:30 Mark Abraham : > > > Hi, > > > > Either your topolo

Re: [gmx-users] bonded parameter

this means that "bonded parameter" not necessary for my work or that my work is wrong 2015-08-12 22:53 GMT+04:30 Mark Abraham : > Hi, > > Either your topology doesn't use those parameters, or the interactions that > use them were converted to constraints by the settings in your .mdp file. > > (B

Re: [gmx-users] Change to umbrella sampling pull code

Hi, On Wed, Aug 12, 2015 at 6:20 PM Nash, Anthony wrote: > Dear all, > > This is the first time I¹ve ran pull code (for umbrella sampling) since > the change from Gromacs 4 to gromancs 5. I¹ve noticed some difference in > the .mdp key-value parameters. Could I have a sanity check on the values >

Re: [gmx-users] bonded parameter

Hi, Either your topology doesn't use those parameters, or the interactions that use them were converted to constraints by the settings in your .mdp file. (By the way, it is better to talk about a "stage" of an MD workflow, as "step" can be misunderstood to mean an integration step.) Mark ‪On We

Re: [gmx-users] bonded parameter

but I delete bonded parameter from my force field in spite of this topology file was created and all step is runing without any error 2015-08-12 21:56 GMT+04:30 Maryam Kowsar : > Hi Hassan, > For making a topology(.top) file all parameters of your forcefield is > needed. > > On Wed, Aug 12, 2015

Re: [gmx-users] Force constant

Hi, To which I would also suggest adding checks of any available experimental quantities (e.g. density, heat of vaporization) and considering carefully following the techniques used in parametrizing the parent force field. Mark On Wed, Aug 12, 2015 at 5:24 PM André Farias de Moura wrote: > sur

Re: [gmx-users] bonded parameter

Hi Hassan, For making a topology(.top) file all parameters of your forcefield is needed. On Wed, Aug 12, 2015 at 9:37 PM, حسن هاشم زاده wrote: > Hi > > ?Which step of simulation the bonded parameters of available in a force > field will be used > -- > Gromacs Users mailing list > > * Please sear

[gmx-users] bonded parameter

Hi ?Which step of simulation the bonded parameters of available in a force field will be used -- 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_Lists

[gmx-users] Change to umbrella sampling pull code

Dear all, This is the first time I¹ve ran pull code (for umbrella sampling) since the change from Gromacs 4 to gromancs 5. I¹ve noticed some difference in the .mdp key-value parameters. Could I have a sanity check on the values below. Also, given that I want a harmonic potential between the two gr

Re: [gmx-users] Force constant

sure, it can be done (not published yet, but we did it for a small molecule recently - CH2I2): (1) chose an appropriate level of theory and basis set, perform geometry optimization and frequency calculation (mind that each combination of level of theory and basis set have its own scaling factor to

Re: [gmx-users] Pdb file

I mean potential energy of system (1600 argon atoms) is positive after energy mininization . On 12 Aug 2015 16:58, "Vitaly V. Chaban" wrote: > L_BFGS > > > > > On Tue, Aug 11, 2015 at 11:37 PM, Sunil Ghimire > wrote: > > I created the pdb file by genconf but the system was not minimized, i got >

Re: [gmx-users] Distance restrain with dummy atom

Dear Justin, Thanks for the reply. As you suggested I have tried with flat-bottomed position restraint. Unfortunately, the water molecules were seen to be moving to vacuum that leads to membrane distortion. The methodology I adopted is as follows, 1. I done 5 ns equilibration of protein-membrane-

[gmx-users] Force constant

Dear all, I have to write the .itp file for my molecule, and I have problem with finding the correct value for force constants. Is it possible to calculate bond/angle force constant from ab initio calculation? Thank you in advance Mehrnoosh -- Gromacs Users mailing list * Please search the arch

[gmx-users] Charged group problem

Dear users, My system contains peptide + TFE + water in an octahedron box. I am using oplsaa.ff I am trying to do EM but running this command grompp -f em.mdp -c C22_TFE-W.gro -p topol.top -o em.tpr the next error message come up WARNING 1 [file em.mdp]: The sum of the two largest charge gro

Re: [gmx-users] Charmm 36 parameter file for gromacs

Dear Dr. Justin I got your means and it is very helpful for me. Thank you so much :) Sincerely, Tuong Vy 2015-08-12 21:23 GMT+09:00 Justin Lemkul : > > > On 8/12/15 8:20 AM, Vy Phan wrote: > >> Dear Dr Justin and Gromacs User, >> As I mentioned in the previous email , I download the parameter f

Re: [gmx-users] Charmm 36 parameter file for gromacs

On 8/12/15 8:20 AM, Vy Phan wrote: Dear Dr Justin and Gromacs User, As I mentioned in the previous email , I download the parameter from this website which was build for all-atom simulation ( http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file The list does not accept att

Re: [gmx-users] Charmm 36 parameter file for gromacs

Dear Dr Justin and Gromacs User, As I mentioned in the previous email , I download the parameter from this website which was build for all-atom simulation ( http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file below . I have a confusion with Tielema's website. I use this for run

Re: [gmx-users] sample working DNA file?

On 8/12/15 6:07 AM, toannt wrote: Hi all, I have problems with a simple setup of DNA system. I try some programs to generate DNA pdb file. Some pdb output doesn't work. Some requires a lot of manual edits. I finally got a pdb file working but I still have some problems with long "bonds". Does

Re: [gmx-users] pdb file for united atom force fields

On 8/12/15 12:46 AM, faride badalkhani wrote: Dear Gromacs users, I need to work with a united atom FF, but I have defined all the Hydrogens in my pdb file. Does it cause any problem in MD procedure? Well, the UA force field won't use (most of) the H, so they obviously need to be removed.

Re: [gmx-users] Charmm 36 parameter file for gromacs

On 8/11/15 10:15 PM, Vy Phan wrote: Dear Dr. Justin and Gromacs User, Thank you so much for your helps. When I use charmm36 ff to generate the topology for lipid (DOPC). I got many warning "Warning :Long bond " And after get the topology, the total charge is very high (+888 e for DOPC bilayer

Re: [gmx-users] Pdb file

L_BFGS On Tue, Aug 11, 2015 at 11:37 PM, Sunil Ghimire wrote: > I created the pdb file by genconf but the system was not minimized, i got > positive potential energy. What may be the problem? > On 11 Aug 2015 19:38, "Mark Abraham" wrote: > >> Hi, >> >> gmx genconf on a small box with a single

[gmx-users] sample working DNA file?

Hi all, I have problems with a simple setup of DNA system. I try some programs to generate DNA pdb file. Some pdb output doesn't work. Some requires a lot of manual edits. I finally got a pdb file working but I still have some problems with long "bonds". Does anybody have a sample working DNA

Re: [gmx-users] Local pressure of water

Please check the link below, http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure On Tue, Aug 11, 2015 at 11:16 PM, 折晓会 wrote: > Dear all,I am simulating polarizable water with Gromacs 5.0.5. I am > wondering if it is possible to calculate the pressure profiles along

Re: [gmx-users] Pdb file

Hi, When can a single argon-argon interaction have a negative potential energy? Mark On Wed, Aug 12, 2015 at 4:37 AM Sunil Ghimire wrote: > I created the pdb file by genconf but the system was not minimized, i got > positive potential energy. What may be the problem? > On 11 Aug 2015 19:38, "M

[gmx-users] gmx cluster cut off

Dear all, I have done protein with three different inhibitor for 100ns simulation and would use the most populated structure for further analysis. What i wonder is how do i select the perfect cut off value to choose the most populated structure from 100ns? Is that following command can prov