[gmx-users] principal moments of ellipsoid

Hi, I want to study the shape change of a macromolecule which seems like a ellipsoid. So, I need obtain the three principal moments of the molecules. Is the command of g_gyrate helpful for me? The sum of the three principal moments should be equal to the Rg^2. However, I used the command

Re: [gmx-users] principal moments of ellipsoid

Not R_x, R_y, and R_z. What I want to obtain are the three three principal moments of the ellipsoidal macromolecule. They are different quantities. 2011/5/10 Erik Marklund er...@xray.bmc.uu.se Mark Abraham skrev 2011-05-10 12.31: On 10/05/2011 8:23 PM, lammps lammps wrote: Hi, I want

Re: [gmx-users] principal moments of ellipsoid

Yes, However, what does the data in axis1.dat, axis2.dat, axis3.dat and moi.dat mean? Should I put the center-of-mass of the molecule in the origin when using the g_principal command? It seems that the inertia is calculated relative to the origin. May be my understanding wrong. -- wade --

[gmx-users] How to control the temperature when using an electric field?

Hi, I want to use the option of E_x = 1 0.01 0 to add an electric field to the simulated system in NVT ensemble. Because there should exist an no zero velocity of center-of-mass in the x direction. It seems that it is wrong to directly use the nose-hoover to control the temperature. it is

[gmx-users] how to write a rtp file for amido amine

Hi everybody, I want to use pdb2gmx command to create a .gro file and a .top file for PAMAM whose repeat unit is amidoamine ( attached ). / ---CH2--CH2--CO-NH-CH2-CH2-N(see the attached figure) \

Re: [gmx-users] how to write a rtp file for amido amine

...@anu.edu.au - Original Message - From: lammps lammps lammp2fo...@gmail.com Date: Saturday, October 9, 2010 19:27 Subject: [gmx-users] how to write a rtp file for amido amine To: Discussion list for GROMACS users gmx-users@gromacs.org Hi everybody, I want to use pdb2gmx command

Re: [gmx-users] how to write a rtp file for amido amine

again. 2010/10/9 Justin A. Lemkul jalem...@vt.edu lammps lammps wrote: Hi Mark, Thanks for your reply. But, I do not know the meaning of the columns in specbonds.dat. I also do not find any information in the manual 4.0. Could you provide something about the specbonds.dat or give some

Re: [gmx-users] how to write a rtp file for amido amine

get it Thanks very much!! 2010/10/10 Justin A. Lemkul jalem...@vt.edu lammps lammps wrote: Thanks for Mark and Justin's help. But I have new questions as follows: CYS SG 1 HEMEFE 2 0.25CYS2HEME 1.residue name A 2.atom name A 3.number of bonds

[gmx-users] the total charge of a neutral molecules is not zero

Dear everyone, I use OPLS AA field to deal with a neutral molecules. However, the Total charge is 8.500 e, not zero. Are there other reasons for this problem except giving a wrong parameter due to my carelessness. I can not find the errors. Any suggest is appreciated. Thanks in advance. --

[gmx-users] OPLS-AA force field

Hi everybody, I want to use OPLS-AA force field to do simulation for dendrimer(see the attached files for figure and .pdb). If the pH4.0，the tertiary amines on the dendrimer will be protonated, i.e. (CH2)3-N will be changed to (CH2)3-NH+. Now, I have two questions as follows. 1. How can I use

[gmx-users] mean force.

Hi everyone, I use umbrella sample and g_wham to get potential of mean force. However, I also want to compute the mean force. How can I deal with this? Can I get it through calculating the average of data in pullf.xvg file? Thanks in advance. Wende -- ;spring point is equal to

[gmx-users] g_order in GMX4.05

Hello everyone, I use the g_order to get the order parameter of the tails( C1A, C2A, C3A, C4A) of DPPC. The are 100 molecules of DPPC 1. I use the make_ndx -f dppc.trr -n index to produce the index file. a C1A a C2A a C3A a C4A del 0-3 Q_1: Is the method right to produce the index file?

Re: [gmx-users] fix a group in truncated octahedron

Sorry for this. Thanks for your kind reply. That is the answer of my question. Actually, I only want to make sure whether the command of energygrp_excl has the ability not to calculate the force in the group. The manual about energygrp_excl seems not talk about how to deal with the force.

[gmx-users] fix a group in truncated octahedron

Hi GMX users, I want to fix a group in a truncate octahedron. How can I dealt with the question below, There is One spherical rigid body consists of face-center cubic lattices fixed in the center of the box. I do not want to calculate the force and energy between the paritcles of this rigid

[gmx-users] fix a group in truncated octahedron

Hi GMX users, I want to fix a group in a truncate octahedron. How can I dealt with the questions below, 1. I hope the box corresponds to an inscribed circle of cubic of size 40*40*40, how to calculate the box vectors? 2. One spherical rigid body consists of face-center cubic lattices is fixed

[gmx-users] fix a group in truncated octahedron

Hi, I want to fix a group in a truncate octahedron. How can I dealt with the questions below, 1. I hope the box corresponds to an inscribed circle of cubic of size 40*40*40, how to calculate the box vectors? 2. One spherical rigid body consists of face-center cubic lattices is fixed in the

[gmx-users] steered MD simulation for calculating the PMF

Hello, I want to use the Steered molecular dynamics simulations to calculate the PMF with Gromacs. How could I write the pull code? Are there some examples? And what files the GMX will create when running the SMD code? Then how to obtain the PMF after full running? Is there any command for

[gmx-users] How to calculate the PMF?

Dear all, It is the first time that I use gromacs 4.04 to calculate PMF. I have some question needed to be clarified. 1. ; ; pull code for PMF pull= Unbrella;unbrella,constraint

[gmx-users] how to obtain the hydrogen bond energy?

Hi, I used the OPLS-AA FF to simulate the PEO and water systems. The are hydrogen bond between PEO and water. I want to obtain the average energy of these dydrogen bond. How can I do? Should I calculate the free energy? Any idea is appreciated. Thanks in advance. -- wende -- gmx-users

[gmx-users] reduced units

Dear, I want to do stochastic simulations in the framework of Langevin dynamics using Gromacs with the reduced units. The questions are: 1. How to turn on the reduced units? Is there any parameters for setting? 2. If I use the reduced temperature of 1, should the ref_t in the .mdp file be the

[gmx-users] how to create a PEO Residue database

Hi everyone, The structural formula of PEO is CH3-- O- CH2 - CH2 - (O - -CH2 - CH2 )n - O - -CH2 - CH2 - O - CH3 I have obtain all the OPLS-AA FF for PEO from a paper such as atomtypes, bondtypes, angletypes, and dihedraltypes. Then I have a .PDB of PEO. I need a residuce to create .top and

[gmx-users] PEO and OPLS-AA FF in gmx

Hi, I want to simulate a PEO chain in water using OPLs-AA FF in Gromacs. I have created a .PDB file using Material Studio, but I seems that the pdb2gmx can not dealt with it because of the error Residue 'xx' not found in residue topology database The question is how can I obtain the .top and

[gmx-users] question about g_rdf

Dear everyone, I use the command (g_rdf -f traj.trr -s md.tpr -o rdf_12.xvg -sq sq_12.xvg -b 1000 -bin 0.01 -cut 1.2 -grid 0.05 ) to calculate the RDF There are two questions: Question_1: Why should we do the three times selections[ the red line], Reading file md.tpr, VERSION 4.0.4 (single

[gmx-users] 43A1-S3 FF

Dear gmx developer, I have read the paper* An Improved United Atom Force Field for Simulation of Mixed Lipid Bilayers J. Phys. Chem. B 2748 2009, 113, 2748–2763* Is the new force field (43A1-S3) can instead of the FF of Berger et al. for lipid simulations? When will it be incorporated in

Re: [gmx-users] about epsion_surface

I want to know the arithmetic of GROMACS for dealing with epsion_surface. Any ref. paper? Because I donot know Why the manual give a note about this parameter: Be careful - you shouldn’t use this if you have free mobile charges in your system. Thanks in advance. -- wende

[gmx-users] epsion_surface

Hi, I do not know why the manual give a note about the parameter of epsion_surface : Be careful - you shouldn’t use this if you have free mobile charges in your system. WHY? Could some kind people give me an explanation or some references? Thanks in advance.

[gmx-users] fatal error when using Martini CG force field

When I use CG martini force field to do simulation, and use the example of Martini website. There are many warnings when grompp the mdp file: -- WARNING 4 [file mem16.top, line 41]: For proper thermostat integration tau_t (0.1) should be more than an order of magnitude larger than

[gmx-users] Re: fatal error when using Martini CG force field

I use the gmx4.04 version. The detail error information is as follows. May be there is a bug in domain decompostion method because someone met this problem beforce. Not all bonded interactions have been properly assigned to the domain decomposition cells A list

Re: [gmx-users] Problem in Martini simulation with gromacs version 4.0.4 works fine with gromacs 3.3.1 error G96Angle of 2395 missing

I  meet the same problem. Have you delt with it? What's the Matter? Thanks in advance. -- wende ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] zero surface tension

Hello everyone, In the literature, Many reports use the lateral and normal pressures independently coupled to a pressure of 1 bar for bio-membrane simulations. I want to know whether it can guarantee the zero surface tension of the membrane. If not, which situation it can not guarantee. Any

[gmx-users] about epsion_surface

Dear, I do not know where should I have to use the epsion_surface? The system include a CG membrane, a charged macromolecule above the membrane and some counterions ? It is suitable to using this parameter epsilon_surface = 1? It is appricated if some one tell me something about how to use this

[gmx-users] say something about the pull geometry of cylinder

Hi , I can not fully understand the picture of parameter of pull geometry of cylinder. Who can say something about it, Thanks in advance. Thanks in advance. - pull geometry cylinder Designed for pulling with respect to a layer where the reference COM is

[gmx-users] How to understand the pull geometry of cylinder

Hi everyone, My colleague and I can not understand the picture of parameter of pull geometry of cylinder. How to determine the reference COM? How does the pulled group move? It is apprecited if someone gives me a simple picture of the parameter. A sketch map is OK. Thanks in advance.

[gmx-users] about martini forcefield(MFF)

Dear , I do MD simulation with Martini Force Field. There are about 2048 DPPCs in my system. But I don't know how many.water molecules should be added to system of (25 25 17)nm . Is it important that the ratio of water/DPPC for DPPC behavior? Can I add water arbitrarily, such as 7 or more?

[gmx-users] about MARTINI forcefield

Hi MARTINI forcefield users, I am very interesting in using the MARTINI forcefield for simulating my molecules, But I am not very familiar with it. So I hope some kind people can help me about its application. I want to know if It is suitable for the molecules of attached figures. It have TWO

[gmx-users] How to carry out rigid body

Hi everyone, I want to peform CG-MDs with gromacs. In my system, there are some rigid bodies which are composed by hundreds of LJ atoms. Atoms of each rigid body move together in LJ water solution. How can I deal with it? Any suggestion is appreciated. Thanks in advance. -- wende