[gmx-users] conversion xtc to xyz format with openbabel

Hello all, My apologies for these out topic questions Does anybody have already try to convert xtc trajectory into xyz with openbabel? Btw, it seems that pdb file generated with editconf can not be read by openbabel. I obtain the following error : WARNING: Problems reading a PDB file

[gmx-users] Simulations in NVE ensemble with CHARMM36

Dear GMX-users I have done a 90 ns long simulation of a heterogeneous system (SPCE water, phospholipids and a hydrophobic solvent) in NPT ensemble (298 K at 1 bar) with GROMACS4.6.5. to compute related dynamical properties, I would like to continue this simulation in NVE. But I am puzzled to

Re: [gmx-users] Simulations in NVE ensemble with CHARMM36 - update

. The cluster pair list does have a buffering effect, but choosing a larger rlist might be necessary for good energy conservation. Stéphane On 5/7/14, 9:05 AM, ABEL Stephane 175950 wrote: Dear GMX-users I have done a 90 ns long simulation of a heterogeneous system (SPCE water, phospholipids

[gmx-users] Use trjconv in parallel,

Hello, in short : it is possible ? I use the gromacs v4.6.5. Thanks Stéphane -- 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

Re: [gmx-users] Use trjconv in parallel

Thanks for your quick and also fast (;)) reply, Carsten. Stéphane -- Message: 4 Date: Wed, 2 Jul 2014 10:55:45 + From: ABEL Stephane 175950 stephane.a...@cea.fr To: gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se

[gmx-users] conversion of the AMBER parameters to GROMACS with negative barrier height values

Hello all, I am trying to convert some GLYCAM parameters to do simulations with the GROMACS code. In the glycam force field, several dihedral terms have negative barrier height values, for instance, -20 in the following parameter: Os-Cj-Cj-Ha 1 -20.00 0.0 2

[gmx-users] Naughty Vacuum Bubble in our Vesicle

Hello Bjorn I don't know if it related to your problem, but I see a typo in our mdp file for the pressure coupling: Pcoupltype = isotropic ;semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 4.0 4.0 compressibility

[gmx-users] how to remove water molecule inside micelle

Hello, It is not a really problem, since the water will move during the simulation (due to the hydrophobic effect), but It may take for that all the water left the micelle center. So I suggest you to use genbox with the following arguments -shell or -vdwd (see the genbox manual). An other

[gmx-users] command line with gangle

Hello all, I have a stupid question : I would like to use gangle (v5.0.4) with the following command line gmx_mpi gangle -f conv3.xtc -s 60_SDS_CHARMM_5_NAP_504_run_1.tpr -n paipai_dist_theta.ndx -g1 plane -group1 -g2 plane -group2 -oav test_angle.xvg -b 39000 -e 4 test_angle.txt

[gmx-users] command line with gangle

Many thanks, Teemu it works Stephane -- Message: 3 Date: Fri, 20 Mar 2015 18:05:49 +0200 From: Teemu Murtola teemu.murt...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] command line with gangle Message-ID:

[gmx-users] infinite force at the membrane lipid

Hello, How did you construct your membrane, with CHARMM-GUI? What is the lipid? From my experience, I have found that sometimes CHARMM-GUI does not provide a good starting point for MD. So I would suggest you to : - center the lipids inside the box to have no lipids that cross the box limit

[gmx-users] Reverse micelle clustering issue

Hello To center your RM inside teh box you could use to successive trjconv commands with pbc cluster and mol in index.ndx 0 : all 1 AOT 2 water 3 AOT_Water 4 ISO 1 -- select 1 1 0 (or 2 2 0) echo 1 1 0 | trjconv -f my_initial.xtc -s my_tpr.tpr -pbc cluster -ur compact -center -o

Re: [gmx-users] top parameters for pluronic f127 (Andrian Saputra)

Hi, Before to compute the partial charges , you have to optimize the molecule. It may be very difficult if you have a large molecule (> 100 atoms). So for polymers with reapeated units, it is always advisable to separate the molecule into similar molecular blocks. It is straighforward for

[gmx-users] grompp not enough parameters

Hi Marlon, If you change the comma into a point in the force constant values it should work Good luck Hello, I'm trying to use the amber03 ff to simulate a protein with iron clusters. I got the right parameters from a paper but then grompp tells me: "ERROR 1 [file

[gmx-users] Angle between a vector and the normal to a sphere

Hi all, Is there a command/tool in a gromacs to compute the angle between a vector defined defined two atoms molecule and the normal to a sphere defined by a set of atoms for instance water ? if yes, how I use a version of gromacs > 5.0 Thanks Stéphane -- Gromacs Users mailing list *

[gmx-users] Angle between a vector and the normal to a sphere

OK thanks Yu, I have another question how to select the water sphere center dynamically With g_select? S - Hi St?phane, gmx gangle may be what you need. http://manual.gromacs.org/programs/gmx-gangle.html -Yu 2016-05-31 13:22 GMT+02:00 ABEL Stephane

[gmx-users] empty aminoacids.n.tdb and aminoacids.c.tdb files for Amber99*

Hello again I have noticed that in case of the amber* forcefields (in gromacs v504) the aminoacids.n.tdb and aminoacids.c.tdb files are empty* so it is not possible to construct easily a capped AA with the pdb2gmx -ter command without using a rtp file (and it is very painful). So does anyone

Re: [gmx-users] pdb2gmx error

Indeed Justin I have tried to add the entries for the capped groups in the Amber99SB-ILDN force field (like in the charmm*.ff) since they are not present in aminoacids.n.tdb and aminoacids.c.tdb, so I think I have broken something Stéphane On 4/5/16 6:47 AM, ABEL Stephane 175950 wrote

Re: [gmx-users] update .hdb file

Hello Shahla, We have developed a tool for GROMACS (rtp2hdb) that can construct a hdb table file for you with any rtp file. Please contact me contact me off list if you are interested Best -- Message: 5 Date: Sat, 9 Apr 2016 08:49:05 -0400 From: Justin Lemkul

[gmx-users] pdb2gmx error

Hello, When i use pdb2gmx (v.504) and 12 AA long peptide with the Amber99SB-ILDN force field, I have the error : Fatal error: tpA = 53191, i= 0 in print_atoms I have no idea what does this message mean. Could you help me? Thanks -- Gromacs Users mailing list * Please search the archive

[gmx-users] Reaction Field approach with GROMACS

Hi All, I have a question about the reaction field approach used by GROMACS. I have seen that in earlier version (V.4.6.X andn 4.5.3) there was a bug with the Reaction Field approach (http://redmine.gromacs.org/issues/1400). It is corrected in the GROMACS version than 5.0 or in lastest

[gmx-users] problem with backward to construct a CHARMM36 model

Dear all, Sorry in advance if the following message does not follow the netetiquette (my message was already post in the Martini forum) but since more gromacs users read this mailling list than the Martini one, I think that probably some users may help me to resolve my problem. I am

[gmx-users] PBC issues with membrane-peptide simulation

Hi, it is not an issue !! To resolve your problem you could simulate two bilayer in box and insert the peptides between them. HTH -- Message: 6 Date: Wed, 9 Nov 2016 16:07:26 +0530 From: Abhi Acharya To:

[gmx-users] Save the velocities a subset of atoms in a trr file during a simulation

ello, A quick question : It is possible to save the velocities (in a trr file) for only selected atoms "during" a simulation as we can do in case of the xtc files by using a the mdp option compressed-x-grps? Thanks S -- Gromacs Users mailing list * Please search the archive at