[gmx-users] SWCNT interaction with the outside of an ion channel

Hi dear gromacs users, I am planning to study the interaction between a SWCNT and the outside of an ion channel, in order to do this i am preparing a Umbrella Sampling Simulation, were i put the CNT, (3nm or 2nm) from the ion channel's pore, and the CNT axis is parallel to the pore axis, in ord

Re: [gmx-users] Gromacs 5 umbrella sampling

del Valle El 8/04/2014, a las 9:57, "Justin Lemkul" escribió: > > > On 4/8/14, 9:42 AM, Andres Ortega Guerrero wrote: >> Perhaps this problem is solved with gromacs 5.0 ? > > What problem? Please leave enough context to make th

Re: [gmx-users] Gromacs 5 umbrella sampling

Perhaps this problem is solved with gromacs 5.0 ? Andrés Ortega Ing. Electrónica Universidad del Valle -- 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

Re: [gmx-users] Gromacs 5 umbrella sampling

could affect that much due to this bias(do you think so?) , but If I have time try to get both using gromacs 5 , Thanks again Andrés Ortega Ing. Electrónica Universidad del Valle El 7/04/2014, a las 20:45, "Justin Lemkul" escribió: > > > On 4/4/14, 10:48 AM, Andr

Re: [gmx-users] First release candidate for GROMACS 5.0 is available

Andres Ortega -- 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 * For (un)subscribe requests visit

Re: [gmx-users] Gromacs 5 umbrella sampling

Thank you Justin, I will appreciate the help with this doubt, of the reference group, that is not 0 , is 26 in the index file, or the appropiate definition of the reference group thanks -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Gromacs 5 umbrella sampling

i am aggre with you Justin But when i used pull_group0_name= protein2pull this warning appear : WARNING 1 [file pull_npt.mdp, line 70]: Unknown left-hand 'pull_group0_name' in parameter file and if i used pull-coord1-groups = 26 1 26 is the index number of the protein2pull in the in

Re: [gmx-users] Gromacs 5 umbrella sampling

I'm sorry Justin, My mistake, when i use this pull code, using grompp, with this pull code ; Pull code pull= umbrella pull_geometry = direction ; ;pull_vec1 = 0.0 0.0 1.0 ; pull_coord1_vec = 0.0 0.0 1.0 ; ;pull_dim= N N Y pull_start = yes ; def

[gmx-users] Gromacs 5 umbrella sampling

Dear Gromacs User, i am trying to use US, with gromacs 5, I was trying to do a position umbrella sampling so this is my pull code, but i get an error about the pull-coord1-groups, there's no nome group0 and group1 , so how should i define this, or in pull-coord1-groups are the numbers of the grou

Re: [gmx-users] Flat-bottom potentials

thanks Justin, in the Manual-5.0 i dont see the tool, i am assuming that the .itp file , is generated by a tool similar as genrestr as in older version?? Andrés Ortega -- Gromacs Users mailing list * Please search the archive at http://www.gromac

[gmx-users] Flat-bottom potentials

Dear Gromacs Users, I was wondering if you know how to implement or modify the gromacs code in order to do a flat-bottom quadratic potential in the xy plane in order to restraint a molecule in a cylinder? thank you in advance , Andrés Ortega -- View this message in context: http://gromacs.

Re: [gmx-users] Umbrella pulling Drug + Ion channel

Thank you Justin i was wondering if you could, help with the doubt of the use of group0: i will use the entire PROTEIN but considering that the COM is not in the middle of the ion channel's pore , and the PMF of the ligand crossing the pore, i assumed that this distances doesn't affect my c

Re: [gmx-users] Umbrella pulling Drug + Ion channel

rug + Ion channel > > > > On 3/25/14, 8:15 AM, Andres Ortega Guerrero wrote: > > Yes during Equilibration, the drug and the channel was restraint, yesterday > > , i tried changing the pull_geometry to position > > and it worked, i think that maybe there was problem wit

Re: [gmx-users] Umbrella pulling Drug + Ion channel

Yes during Equilibration, the drug and the channel was restraint, yesterday , i tried changing the pull_geometry to position and it worked, i think that maybe there was problem with my cylinder configurations , this was my position configuration, considering this, i might think that theres not a

Re: [gmx-users] Umbrella pulling Drug + Ion channel

The structure was equilibrated by an 30 ns NPT, and the structure is well equilibrated, in the .log file appear this Step Time Lambda 8000 16.00.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih.

[gmx-users] Umbrella pulling Drug + Ion channel

Dear gromacs users, i ´ve beem trying to get the geometries of a drug molecule permeating an ion channel, the drug molecule is in a greater Z position than the Protein, but i always get the error :"Segmentation fault (core dumped)" this is my .mdp title = Umbrella pulling simulation DOX ; Ru

[gmx-users] Pulling code

Dear Gromacs Users, My system consist of a proteins ( membrane channel) and a drug (DOX) and i am trying to run a pull_md in order to force the drug to permeate the channel, but, the channel size and the durg molecule are closed, so i've been reading , i dont know if i should use constraint to

Re: [gmx-users] missing residues in PDB file

You could add them with modeller or rosseta, Andrés Ortega Ing. Electrónica Universidad del Valle El 19/03/2014, a las 14:36, "Guo, Yanan" escribió: > Hello dear gmx-users, > > I want to transform a .pdb file to a .gro file using pdb2gmx. But there are > some missing residues in my .pdb f

Re: [gmx-users] NVT problem

Box, i deleted some residues located at the terminal (inside the membrane) , so i think this could be one reasson of the problem. Thanks again, Thanks Andres Ortega > Date: Sat, 15 Mar 2014 18:04:07 -0400 > From: jalem...@vt.edu > To: gmx-us...@gromacs.org > Subject: Re: [gm

Re: [gmx-users] NVT problem

should i prepare again the .gro files? Thanks in advance Justin, Andres Ortega Universidad del Valle (Colombia) Bionanoelectronics Research Group > Date: Sat, 15 Mar 2014 16:02:43 -0400 > From: jalem...@vt.edu > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] NVT problem >

Re: [gmx-users] NVT problem

that was missing Thanks Justin > Date: Sat, 15 Mar 2014 15:41:11 -0400 > From: jalem...@vt.edu > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] NVT problem > > > > On 3/15/14, 3:37 PM, Andres Ortega Guerrero wrote: > > Thank you Justin for Your Help,

Re: [gmx-users] NVT problem

o: gmx-us...@gromacs.org > Subject: Re: [gmx-users] NVT problem > > > > On 3/15/14, 2:19 PM, Andres Ortega wrote: > > HI , Dear Gromacs Users, > > > > I´ve been trying to run a NVT simulation, in order to equilibrate my system( > > POPC + IONCHANNEL + SOL_IO

[gmx-users] NVT problem

with my mdp file, this is my .mdp , i was wondering if you could help me and give me some advices to solve this Thanks in advance for your time and attention , Andres Ortega title = NVT equilibration for channel_dox define = -DPOSRES -DPOSRES_DOX ; position restrain the protein

[gmx-users] SETTLE and LINCS

Hi Dear Gromacs Users, i have read different post, of how to use settle for water and other constrain algorithm like shake or lincs for non-water bond, this can be use by adding -DFLEXIBLE, lincs non-water ? In old post, some of you said, that Flexible model should be use only for EM , and n

[gmx-users] Neutralize or add an Ions Concentration for a Membrane Simulation?

Hi Dear Gromacs Users, i would like to ask you something, My system consist of an ion channel , and a drug molecule, i´m preparing a umbrella simulation, to study the PME between the protein and the molecule, so , i´ve been reading papers, and some of them just add ions to neutralize the system

[gmx-users] Error Mdrun

Dear Gromacs Users, I was trying to run a simulation , but this NOTE came out: 1 GPU detected: #0: NVIDIA GeForce GT 330, compute cap.: 1.2, ECC: no, stat: incompatible (This mean i cant use this GPU, or GROMACS it is not install well?) Thanks in advance for the help Andres Ortega

Re: [gmx-users] dihedral doubt

I forgot to mention that are Ryckaert-Bellemans form dihedral for OPLS Force Field Andres Ortega From: og_andre...@hotmail.com To: gmx-us...@gromacs.org Subject: RE: [gmx-users] dihedral doubt Date: Sat, 1 Mar 2014 23:54:06 + Thanks Justin for your help, i will modify the i j k l of the

Re: [gmx-users] dihedral doubt

Thanks Justin for your help, i will modify the i j k l of the dihedral in my topology to correspond to the bonded.itp Thanks again Andres Ortega > Date: Sat, 1 Mar 2014 18:39:04 -0500 > From: jalem...@vt.edu > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] dihedral doubt &

Re: [gmx-users] dihedral doubt

Thanks Justin for the advice and help, So i have to add in the bonded.itp O_2 C_2 CT OH with the parameters? or in the topology file (molecule) , y define the dihedral like OH CT C_2 O_2 ??? Thanks in advance Andres Ortega > Date: Sat, 1 Mar 2014 18:11:31 -0500 > From: jalem...@vt.ed

[gmx-users] dihedral doubt

Hy Dear Gromacs Users, i have a question , i´m preparing a topolgy, but i need a dihedral i need O_2 C_2 CT OH, i could find it, but i find OH CT C_2 O_2 , i know that the order oof i j k l, is not the same, but there a way to use it i think that if i do this , is a big mistake.. can you help

Re: [gmx-users] .gro File manipulation

;Mark Abraham" escribió: > Hi, > > I think you want genbox -cs membrane -box x y z (and a lot of > equilibration). > > Mark > > > On Thu, Feb 13, 2014 at 6:13 AM, Andres Ortega wrote: > >> Dear Gromacs Users, >> >> I hava a membrane channe

[gmx-users] .gro File manipulation

Dear Gromacs Users, I hava a membrane channel in a .gro file, but the -n and -c terminal are bigger, i mean the channel box is bigger( in x and y) than the membrane (512 POPC) , my 512 POPC is created using genconf with a 128POPC so i create a 1152 POPC with genconf nbox 3 3 1 , but there are to

[gmx-users] OPLS added parameters

Hi, Dear Gromacs Users I have a little doubt, is about opls parameters here http://virtualchemistry.org/gmld.php there are some opls topologies, and when i checked it there is a oplsff.itp, with some interaction added and check Gromacs 4.6.5 and there are not included, it is necessary to add th

Re: [gmx-users] Umbrella Sampling Tutorial

Thanks ! Andrés Ortega Ing. Electrónica Universidad del Valle El 13/01/2014, a las 8:59, "Thomas Schlesier" escribió: > Since the spring has a finite force constant, it is quite naturally that one > observes fluctuations in the distance (between reference and pulled group) > and forces.

[gmx-users] Umbrella Sampling Tutorial

Hi, Dear Gromacs Users I was running de Umbrella Sampling Tutorial, and when i get the frames from the trajectory, there are some frames like this: 489 5.3776196 490 5.3817739 491 5.3752654 492 5.3619911 493 5.3890083 494 5.3918220 495 5.4115819 496 5.4074620 497

[gmx-users] Gemcitabine topolgy for OPLS

Hi, i´m trying to run a MD with Gemcitabine using OPLS /AA ff, to get the .itp, should i use topolgen , and then calculate the charges with gaussian ussing ChelpG charges, and replace it, i was wondering if this procedure is correct, algo i´m pretending , to study this molecule with a CNT, and a

[gmx-users] Gemcitabine topolgy for OPLS

Hi, i´m trying to run a MD with Gemcitabine using OPLS /AA ff, to get the .itp, should i use topolgen , and then calculate the charges with gaussian ussing ChelpG charges, and replace it, i was wondering if this procedure is correct, algo i´m pretending , to study this molecule with a CNT, and a m