[gmx-users] RE: How to rescue trr trajectory when two or more corrupted frames exist

Thanks for the reply Chris :). It is not possible to get the data with -b option, since trjconv crashes when it meets the corrupted frame. I never had corruption issues in the past and thereby didn't use gmxcheck early enough to avoid the second corruption. The problems should have occurred in

[gmx-users] How to rescue trr trajectory when two or more corrupted frames exist

Dear Gromacs users, I have some corrupted frames in different trajectories. gmxcheck with .trr trajectories gives extraordinary positions or velocities and with .xtc trajectories gives rise to the magic number error. I am aware of the program gmx_rescue kindly offered to us by its developers. H

[gmx-users] Re: g_msd with input by trjconv -pbc nojump:a concern

other of 0. I would appreciate if someone let me know whether -pbc nojump continuity is unconditional or frequency of saving-dependent. Thank you in advance! Best regards, Ioannis /Flo On Mon, 2012-03-19 at 14:31 +0200, Ioannis Beis wrote: Dear Gromacs users, I have been trying t

[gmx-users] g_msd with input by trjconv -pbc nojump:a concern

Dear Gromacs users, I have been trying to calculate the lateral MSD of lipid molecules within a bilayer. I have performed simulations in a rectangular box with PBC. I have used trjconv with -pbc nojump. I compared results between the initial trajectory and the one generated by trjconv for 6

[gmx-users] g_rdf and lipid bilayer hydration

Dear Gromacs users, I have a question related to the use of g_rdf for the calculation of hydration of a lipid bilayer patch. I used g_rdf with -surf flag (I tried both mol and res) and two index groups: the oxygens of waters as first group and the atoms of the headgroups as second group. I

[gmx-users] Re: How to calculate hydration of lipid headgroups by minimum distance means

et=ISO-8859-7; format=flowed Hi again, On 30/01/2012 10:44 PM, Ioannis Beis wrote: Dear Gromacs users, I am trying to calculate the hydration of lipid headgroups in a lipid bilayer system. More specifically, I would like to find the time-averaged distribution of water molecules around

[gmx-users] Re: gmx-users Digest, Vol 93, Issue 169

GROMACS users Message-ID: <4f26893e.2070...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-7; format=flowed On 30/01/2012 10:44 PM, Ioannis Beis wrote: Dear Gromacs users, I am trying to calculate the hydration of lipid headgroups in a lipid bilayer system. More specifically, I would l

[gmx-users] How to calculate hydration of lipid headgroups by minimum distance means

Dear Gromacs users, I am trying to calculate the hydration of lipid headgroups in a lipid bilayer system. More specifically, I would like to find the time-averaged distribution of water molecules around lipid headgroups by means of the closest distance of the water oxygen from any atom of

[gmx-users] Re: Problem with trjconv and centering bilayer.

t/plain; charset=UTF-8; format=flowed Ioannis Beis wrote: Dear gromacs users, I am trying to center the trajectory of a bilayer in the rectangular simulation box in the frame of my effort to calculate the bilayer thickness with g_dist. According to the visualization, the upper layer of the memb

[gmx-users] Problem with trjconv and centering bilayer.

Dear gromacs users, I am trying to center the trajectory of a bilayer in the rectangular simulation box in the frame of my effort to calculate the bilayer thickness with g_dist. According to the visualization, the upper layer of the membrane lies on the lowest part of the box and the lower

[gmx-users] A special case of cutoffs related to mdrun with -rerun option

Dear GROMACS users, I am interested in using mdrun of a special version of GROMACS 4.0.2 made by Ollila et. al with -rerun option, made so that it can allow calculations of properties related to local pressure in lipid bilayer systems. I have used GROMOS54a7 with Poger parameters, but among

[gmx-users] How to make coordinate file with correct numbering in the atoms when inbetween atoms are removed

Dear gromacs users, It seems that because of my inexperience I have been trapped in a simple-looking labyrinth. I wanted to change a .gro file containing hydrated bilayer, in which I want to remove/modify certain atoms from certain lipid residues, e.g. cutting off a polar head. This kind of

[gmx-users] All-atom topologies for lipid head groups

Dear Gromacs users, I am a new user and I am trying to study the physical properties of the interactions between cytosolic proteins and lipids. I have created the Berger-Gromos combination, as described by Mr. Justin Lemkul in his KALP15 in DPPC tutorial, as well as Berger-OplsAA, as descri

[gmx-users] RE: How to use Inflategro with different lipid types

Hello, I would like to thank Justin and Tom for their kind replies to my question! I believe that by having the gromacs manual as a guide I would manage to bring the bilayer into physiological size by using Justin's advice. However, Tom's advice sounds simpler to implement. Unfortunately

[gmx-users] How to use Inflategro with different lipid types

Dear gromacs users, I am a new user of gromacs. I am currently trying to build a large bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and no protein embedded in it. I have used single lipids from pre-equilibrated bilayers available at Mr. Tieleman's website. The distan