[gmx-users] Regarding error

Dear all gromacs users, I tried the grompp -c 3I40_ion.gro -p 3I40.top -o 3I40_b4em.tpr -f em.mdp and i got the following error. Option Filename Type Description -f em.mdp Input

RE: [gmx-users] Regarding error

I guess you have duplicate the moleculetype entries for CU1 in your topology file. Check your topology file again. You can not have more than one moleculetype definition per molecule type. Cheers, Emmanuel = Emmanuel Birru PhD

[gmx-users] How to install GROMACS in 64-bit?

Dear Sir/Madam, Thanks for the insightful comments from the experts.Follows the steps, I found the source of error: This what I have done: In the following directory /home/softwares/fftw-3.0.1:./configure --enable-shared

Re: [gmx-users] How to install GROMACS in 64-bit?

On 29/05/2012 6:37 PM, a a wrote: Dear Sir/Madam, Thanks for the insightful comments from the experts.Follows the steps, I found the source of error: This what I have done: In the following directory /home/softwares/fftw-3.0.1:

[gmx-users] Possible bug: energy changes with the number of nodes for energy minimization

Hi, I'm running a number of energy minimizations on a clathrate supercell and I get quite significantly different values for the total energy depending on the number of mpi processes / number of threads I use. More specifically, some numbers I get are: #cores energy 1

[gmx-users] hydration layers around protein

Friends, I read in many articles explaining the behaviour of water in the first (or second etc) hydration layers around a protein. I am curious to know if there is any way to obtain/guess the thickness of this layer. How does one defines the thickness ? Thanks, Bala -- C. Balasubramanian --

Re: [gmx-users] hydration layers around protein

One option is to calculate the rdf (radial distribution function g_rdf [-surf]) of water oxygen atoms and find the position of the first few peaks... Il 29/05/2012 12:28, Bala subramanian ha scritto: Friends, I read in many articles explaining the behaviour of water in the first (or second

Re: [gmx-users] Position Restraints of one of the moleculetpye

Ok. My topology: ; Include forcefield parameters #include ./charmm27.ff/forcefield.itp ; Include ligand topology #include ligand1.itp ; Include Position restraint file #ifdef POSRES_1 #include posre_ligand1.itp #endif ; Include ligand topology #include ligand2.itp ; Include Position restraint

Re: [gmx-users] Position Restraints of one of the moleculetpye

On 5/29/12 6:52 AM, Steven Neumann wrote: Ok. My topology: ; Include forcefield parameters #include ./charmm27.ff/forcefield.itp ; Include ligand topology #include ligand1.itp ; Include Position restraint file #ifdef POSRES_1 #include posre_ligand1.itp #endif ; Include ligand topology

Re: [gmx-users] Position Restraints of one of the moleculetpye

On Tue, May 29, 2012 at 12:21 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/29/12 6:52 AM, Steven Neumann wrote: Ok. My topology: ; Include forcefield parameters #include ./charmm27.ff/forcefield.itp ; Include ligand topology #include ligand1.itp ; Include Position restraint file

[gmx-users] How to generate the initial coordinates file?

Hi, all, I am new to Gromacs and MD. I just went through a few tutorials on Gromacs quickly. I have a question now. I know the structure of molecule A and B, such as the atoms compositions and the relative position of the atoms and the charge. Now, I want to use 500 A and 100 B to do the

Re: [gmx-users] How to generate the initial coordinates file?

On 5/29/12 8:46 AM, Bao Kai wrote: Hi, all, I am new to Gromacs and MD. I just went through a few tutorials on Gromacs quickly. I have a question now. I know the structure of molecule A and B, such as the atoms compositions and the relative position of the atoms and the charge. Now, I

Re: [gmx-users] Possible bug: energy changes with the number of nodes for energy minimization

On 5/29/12 6:22 AM, Stephen Cox wrote: Hi, I'm running a number of energy minimizations on a clathrate supercell and I get quite significantly different values for the total energy depending on the number of mpi processes / number of threads I use. More specifically, some numbers I get are:

RE: [gmx-users] How to install GROMACS in 64-bit?

Dear Mark, I have overlook it. Sorry. I have already added the following two sentences in .bashrc file in my home directory (when I login as user). export CPPFLAGS=-I/home/softwares/fftw301/include export LDFLAGS=-L/home/softwares/fftw301/lib Should I type in another

[gmx-users] Re: How to generate the initial coordinates file?

Hi, Justin, Thank you very much for your help. It seems that genbox will need really huge memory even with thousands of molecules. If we want to to further to tens or hundreds of thousands molecules, do we need some cluster to run genbox in parallel? Best Regards, Kai Message: 3 Date:

Re: [gmx-users] Re: How to generate the initial coordinates file?

On 5/29/12 4:19 PM, Bao Kai wrote: Hi, Justin, Thank you very much for your help. It seems that genbox will need really huge memory even with thousands of molecules. If we want to to further to tens or hundreds of thousands molecules, do we need some cluster to run genbox in parallel?

Re: [gmx-users] hydration layers around protein

nice suggestioncoletta for ever PS. Lo so che è un commento inutile, ma qualcosa la devo pur dire :D 2012/5/29 Andrea Coletta andrea.cole...@uniroma2.it One option is to calculate the rdf (radial distribution function g_rdf [-surf]) of water oxygen atoms and find the position of

Re: [gmx-users] How to install GROMACS in 64-bit?

On 30/05/2012 1:50 AM, a a wrote: Dear Mark, I have overlook it. Sorry. I have already added the following two sentences in .bashrc file in my home directory (when I login as user). export CPPFLAGS=-I/home/softwares/fftw301/include export LDFLAGS=-L/home/softwares/fftw301/lib Should I