[gmx-users] different distance calculated by grompp and g_dist when doing umbrella sampling simulations

Dear All: I encountered a problem when doing umbrella sampling. The distance calculated by grompp and g_dist is different, as shown by the following: grompp z component of g_dist(since I am constraining the distance between two groups along the z direction, I should calculate the z component o

[gmx-users] questiones about dihedral restrain

Dear All: I am using gromacs4.5.3 to do umbrella sampling simulation of the residue side chain dihedrals. I used the dihedral restrain method described in the mannual to restrain the dihedral values. The method we used is described as follows: we firs

[gmx-users] MD simulations of covalent bound protein-ligand complex by gromacs

Dear All: I am simulating a complex of protein and ligand, however, the ligand is covalent bound to the protein. I have calculated the charges of the ligand and the non-standard residue by QM method and trying to use the bond parameters in the GROMOS force field. However, I don't know how to ma

[gmx-users] sampling the side chain conformations by MD simulations

Dear All: I am conducting molecular dynamics simulations of a proetin. The side chain conformation of one key residue is important for the protein function and I wang to sampling its conformations and calculate the energy barrier when it changes between different conformations. However, the c

[gmx-users] Re: some questions about side chain dihedral angle sampling

I forget to say that, there are other residues around that residue whose side chain coformations will affect each others, So, it is difficult to use umbrella sampling method Regards - 原始邮件 - 发件人: mirc...@sjtu.edu.cn 收件人: gmx-users@gromacs.org 发送时间: 星期五, 2012年 3 月 09日 下午 4:58:02 主题:

[gmx-users] some questions about side chain dihedral angle sampling

Dear All: I am doing molecular dynamics simulations of a protein. In my system, there is a critical residue which is important for its activity. I want to sample the side chain conformations of this residue, i.e., calculate the most favourable side chain dihedral angles of this residue and calc

[gmx-users] Re: problem of installing gromacs4.5.4

Dear Justin: Thank you very much for your reply, but I have another problem. After I install the fftw package, and remove the argument of the --enable-mpi when installing the gromacs package by using the follow commands: export CPPFLAGS=-I/my_path/ export LDFFLAGS=-L/my_path/ ./configure --pr

[gmx-users] a installation problem of gromacs4.5.4 using mpi

Dear All: I encountered a problem when installing gromacs4.5.4 by using mpi. When I finished the installation successfully, I submit a job by assigning 8 processes. However, the job was not run by 8 processes, by generate 8 same jobs each use only 1 process (I have encountered the same problem

[gmx-users] questions about steer molecular dynamics by using gromacs4

Dear All: I am trying to use steer molecular dynamics simulations to pull a ligand along a channel pore (along the Z axis) by constant rate. I know how to realize this by GROMACS3, however, it seemed that in gromacs4, there are some changes regarding this issues, so I am pasting my pull c

[gmx-users] some problems when using g_membed

Dear All: I am using g_membed command to insert a protein into a membrane bilayer, however, when I run the following command: g_membed -f input.tpr -p topology.top -xyinit 0.1 -xyend 1.0 -nxy 1000 I encountered the following errors: Program g_membed, VERSION 4.5.4 Source code file: constr.c

[gmx-users] use AMBER ff03 force field in gromacs 4

Dear All: I am using GROMACS 4 to do MD simulations of protein-ligand complexes.I encountered some problems when generating the topology file of the ligands. I generate the topology file of ligands by using topolbuild package. The atom types of GAFF force field are assigned to the atoms of

[gmx-users] use AMBER ff03 force field in gromacs 4

Dear All: I am using GROMACS 4 to do MD simulations of protein-ligand complexes.I encountered some problems when generating the topology file of the ligands. I generate the topology file of ligands by using topolbuild package. The atom types of GAFF force field are assigned to the atoms o

[gmx-users] Questions on combination of Berger's united-atom force field for lipid and OPLS_AA force field for protein

Dear All: I am using GROMACS package to simulate membrane proteins. I plan to use Berger's united atom force field (Berger's UA FF) for lipids and OPLS_AA force field (OPLS_AA FF) for proteins. I have read the guide post kindly by Prof. Dr. Chris Neale in previous mailing lists very caref

[gmx-users] topology files for ligands in MD Simulation under OPLS AA force field

Dear All: I am using GROMACS package to do molecular dynamics simulations under OPLS_AA force field. I encounter some problems when preparing the topology files of small molecules (ligands).My questions are as follows: 1, how to chose the atom type of each atom from the ligands? 2, how to

[gmx-users] membrane bilayer simulation by OPLS FF

Dear All: I am using OPLS force field (OPLS FF) to do molecular dynamics simulations. My system contains DPPC lipid, protein and a small molecule. I have the following questions: 1, where can I get the topology files for the DPPC lipids? 2, How to prepare the topology files for the small m

[gmx-users] questions about umbrella sampling

Dear All: I am using umbrella sampling method to calculate potential of mean force and I encountered the following questions: 1, at the *.ppa file, I need to incorporate a parameter indicating the "the position of the pull group will restraint to, relative to the reference group" (i.e., the "pos1

[gmx-users] questions about umbrella sampling

Dear All: I am using umbrella sampling method to calculate potential of mean force and I encountered the following questions: 1, at the *.ppa file, I need to incorporate a parameter indicating the "the position of the pull group will restraint to, relative to the reference group" (i.e., the

[gmx-users] problems when using command "trjconv"

Dear All: I encounter some problems when I am using command "trjconv" to remove the periodic boundary condition. I am doing molecular dynamics simulations of a pentamer, and some of the subunits "jump" from one box to its adjacent one. Thus, I try to remove the periodic boundary condition

[gmx-users] some questions about umbrella sampling

Dear All: I am doing umbrella sampling to calculate energy profile of an drug passing through a ion channel by GROMACS3.3. In order to get right result, I need to choose a reasonable force constant in my simulation, right? I know that, a reasonable force constant should produce enough "ov

[gmx-users] Force constant for umbrella sampling potential

Hello everyone, I would like to know does the harmonic biasing potential for running umbrella sampling in gromacs have a 0.5 in front or is the 0.5 term incorporated into the force constant value that we specify? On other words is the potential V=0.5*k(x-xo)^2 or V=k(x-xo)^2. I am using Grossfie

[gmx-users] g_wham error

Dear All: I did some umbrella sampling and got series of .pdo files. I want to calculate potential of mean force (PMF) by g_wham command. However I encount some problems: when I input the following command: g_wham pull.pdo -o xx.xvg -hist xx2.xvg

[gmx-users] about free energy calculation by LIE method

Dear All: I want do some free energy calculation by LIE method. I read the "GROMACS Tutorial for Drug ? Enzyme Complex" carefully and know the method in gromacs to do free energy calculatin by LIE method. However I found the following words at the end of the tutorial: "In this t

[gmx-users] about PMF calculation

Dear All: I want to do some PMF (Potenial of Mean Force) calculation by AFM pulling method using the pull code to study the unbinding of a protein and a ligand. I want pull the ligand from its binding site and calculate the PMF of the procedure, does it possible? I have r

[gmx-users] about coorelation fluctuation calculation

Dear all: I finished a MD simulation and i want to calculation the correlation fluctuation of the alpha C.Does there any tools that can do this in gromacs package (I have tried g_rmsf -oc , but it doesn't work,specificly, the -oc command give no result) ? Can any one be so k

[gmx-users] estimate the binding free energy. long range electrostatic interaction

> mirc...@sjtu.edu.cn wrote: >> Dear All: >> >> I would like to estimate the binding free energy between a drug >> molecule and its receptor. Inorder to do this, i run a MD simulation in >> which PME method was used to deal with long range electrostatic >> intera

[gmx-users] about estiminating the binding free energy by LIE method

Dear All: I would like to estimate the binding free energy between a drug molecule and its receptor. Inorder to do this, i run a MD simulation in which PME method was used to deal with long range electrostatic interaction. I need to calculate the VDW interaction energy and electorst

[gmx-users] estimate free energy bu LIE method, about long range electrostatic interaction

Dear All: I would like to estimate the binding free energy between a drug molecule and its receptor. Inorder to do this, i run a MD simulation in which PME method was used to deal with long range electrostatic interaction. I need to calculate the VDW interaction energy and electorsta