Re: [gmx-users] Gromacs inquiries

Dear Mark, I used to put ten molecules of hexanol in a box 5 5 1 with the instruction genbox -ci hexanol.gro -nmol 10 -box 5 5 1 -o layer.gro -p hexanol.top. However, now I want to fill up the box 4 4 4 with hexanol molecules. If I change the number 10 in the instruction to 1000 or 1, it will

[gmx-users] how can I get the .top file??

Dear members of gromacs Let you know that I'm a beginner of Gromacs. I am trying to simulate the diffusion problem on some zeolite structure. (especially ZSM-22) From the manual, I knew that the three files are required to get the .tpr input file. I got the .pdb file of my concerned

[gmx-users] About implicit wall...

Dear members of gromacs Hi, I'm a beginner of gromacs. I want to simulate the diffusion problem when the particle diffuses into the cylinder pore which has the implicit wall (with some atoms). The diffusing particle has to be updated during the integration step but the particle on the

Re: [gmx-users] Normal Mode Analysis

I've found that in general ussage of cutt-offs beetwen 0.8-1.2 nm might provide good results. But now I have some problems with minimization of my initial structure Firstly, I've performed steep minimization ( emtool=1000, emstep = 0.01 ) and than CG minimization (emtool=1, emstep =

[gmx-users] orientation restraints in binding free energy calculation

Dear gmx-users: I read some research articles of calculating the binding free energy, still I can not figure out how to get the orientational parameters. If I have the crystal structure of ligand bound protein, so I need to choose three anchor atoms in the protein and three anchor atoms in

Re: [gmx-users] Gromacs inquiries

cuong nguyen wrote: Dear Mark, I used to put ten molecules of hexanol in a box 5 5 1 with the instruction genbox -ci hexanol.gro -nmol 10 -box 5 5 1 -o layer.gro -p hexanol.top. However, now I want to fill up the box 4 4 4 with hexanol molecules. If I change the number 10 in the

Re: [gmx-users] how can I get the .top file??

Kiwoong Kim wrote: Dear members of gromacs Let you know that I'm a beginner of Gromacs. I am trying to simulate the diffusion problem on some zeolite structure. (especially ZSM-22) From the manual, I knew that the three files are required to get the .tpr input file. I got the .pdb file

[gmx-users] difference between restrained and constrained

Dear gromacs users I want to know what is difference between restrained EM and restrained EM or between constrained MD and constrained MD. any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] difference between restrained and constrained

shahab shariati wrote: Dear gromacs users I want to know what is difference between restrained EM and restrained EM or between constrained MD and constrained MD. any help will highly appreciated. http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints -Justin --

Re: [gmx-users] Normal Mode Analysis

On 26/10/2011 7:54 PM, James Starlight wrote: I've found that in general ussage of cutt-offs beetwen 0.8-1.2 nm might provide good results. But now I have some problems with minimization of my initial structure Firstly, I've performed steep minimization ( emtool=1000, emstep = 0.01 )

Re: [gmx-users] About implicit wall...

On 26/10/2011 6:47 PM, Kiwoong Kim wrote: Dear members of gromacs Hi, I'm a beginner of gromacs. I want to simulate the diffusion problem when the particle diffuses into the cylinder pore which has the implicit wall (with some atoms). I don't understand the sense in which it could be an

Re: [gmx-users] Normal Mode Analysis

Mark hello, 2011/10/26 Mark Abraham mark.abra...@anu.edu.au We don't know the sense in which it didn't minimize properly, so there's not much point us guessing. The output value for Epot was -2.0 after steep minimization and -2.5 after CG. Also as the consequense after both energy

Re: [gmx-users] Normal Mode Analysis

On 26/10/2011 11:04 PM, James Starlight wrote: Mark hello, 2011/10/26 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au We don't know the sense in which it didn't minimize properly, so there's not much point us guessing. The output value for Epot was -2.0 after

[gmx-users] position restrained minimization on the one part of a system

Dear all my system contains protein + ligand+ water molecules. protein + ligand = solute water molecules = solvent I want to do minimization energy in 3 steps : step 1) on protein only step 2) on all solute (protein + ligand) step 3) on all system should I use position restrained

Re: [gmx-users] position restrained minimization on the one part of a system

On 26/10/2011 11:24 PM, Atila Petrosian wrote: Dear all my system contains protein + ligand+ water molecules. protein + ligand = solute water molecules = solvent I want to do minimization energy in 3 steps : step 1) on protein only step 2) on all solute (protein + ligand) step 3) on all

Re: [gmx-users] Normal Mode Analysis

Mark, 2011/10/26 Mark Abraham mark.abra...@anu.edu.au Or that your starting structure is not close enough to a sensible minimum for a local gradient-based optimizer to do the job. Look at the atoms with the large forces and see what you can learn. So for that purpose I've done steep

Re: [gmx-users] Normal Mode Analysis

James Starlight wrote: Mark, 2011/10/26 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au Or that your starting structure is not close enough to a sensible minimum for a local gradient-based optimizer to do the job. Look at the atoms with the large forces and

[gmx-users] position restrained minimization on the one part of a system

Dear Mark thanks for your reply you said if pdb2gmx is able to treat the whole system in one pass, then it will write such position restraint files automatically in my system, what pdb2gmx includes are in below: ; Include forcefield parameters #include amber03.ff/forcefield.itp ; Include

[gmx-users] position restrained minimization on the one part of a system

I want to use define = -DPOSRES_Protein_chain_A for step 1. is it true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post

Re: [gmx-users] Normal Mode Analysis

Hi James, Regarding PCA and NMA congruency, they are different things, unless the energy landscape consists of a single harmonic potential well. The principal components and the normal modes will usually correlate quite well, but if the simulation is sampling different energy minima, there may be

Re: [gmx-users] position restrained minimization on the one part of a system

Atila Petrosian wrote: I want to use define = -DPOSRES_Protein_chain_A for step 1. is it true? Not per the topology you posted earlier. Your only option (at this point) for restraining the protein is -DPOSRES, which restrains all the chains. If you want to restrain parts of your

[gmx-users] Adding hydrogens to united atom trajectories

Hi, I'm performing united atom simulations of sugars and lipids and comparing calculated properties like C-H dipolar couplings and order parameters with corresponding results from experiments. To do this I need to calculate the hydrogen postitions of the hydrogens I'm interested in, and have

[gmx-users] position restrained minimization on the one part of a system

Dear Justin thanks for your attention I deleted posre.itp file which pdb2gmx was created (containing all solute).I made a posre.itp (containing only protein) by genrestr. now if I use define = -DPOSRES, gromacs use from my posre.itp. is it true? -- gmx-users mailing list

Re: [gmx-users] position restrained minimization on the one part of a system

On 27/10/2011 12:28 AM, Atila Petrosian wrote: Dear Mark thanks for your reply you said if pdb2gmx is able to treat the whole system in one pass, then it will write such position restraint files automatically in my system, what pdb2gmx includes are in below: ; Include forcefield parameters

Re: [gmx-users] position restrained minimization on the one part of a system

Atila Petrosian wrote: Dear Justin thanks for your attention I deleted posre.itp file which pdb2gmx was created (containing all solute).I made a posre.itp (containing only protein) by genrestr. now if I use define = -DPOSRES, gromacs use from my posre.itp. is it true? Assuming you have

Re: [gmx-users] Normal Mode Analysis

Justin, I've forced with the problem that I could not prorerly minimized my system in the NMA conditions. Even in STEEP minimizaation I could not obtain Epot value lower than +3.00 with that parametries ( I've used KALP peptide as a test input ) ; Parameters describing what to do, when to stop

[gmx-users] Center of simulation box

Dear all, In my simulation, when the simulation box shrinks, the center of box always shift towards the origin even if the center motion is set to removed every timestep. I just wonder if there is an anticipated center position for a given simulation box in gromacs. The box type is dodecahedron

Re: [gmx-users] Center of simulation box

zhenlong li wrote: Dear all, In my simulation, when the simulation box shrinks, the center of box always shift towards the origin even if the center motion is set to removed every timestep. I just wonder if there is an anticipated center position for a given simulation box in gromacs. The

Re: [gmx-users] Normal Mode Analysis

James Starlight wrote: Justin, I've forced with the problem that I could not prorerly minimized my system in the NMA conditions. Even in STEEP minimizaation I could not obtain Epot value lower than +3.00 with that parametries ( I've used KALP peptide as a test input ) The Epot value

Re: [gmx-users] Normal Mode Analysis

I've used double precision. Today I'll copied output because it's done on lab comp but from the output log I've found that minimization was not completed ( e.g when I've calculate Normal Modes with that minimized structure I've obtain message that my system was not minimized properly ) 2011/10/26

[gmx-users] query on OPLS-2005

Hi,   I wanted to check what is actually OPLS-2005 forcefield that is recently being referred often for md simulation. However, I also see that whenever, OPLS-2005 is being referred, it cites a 2001 paper by Jorgensen on OPLS forcefield. So, what is actually OPLS-2005? So, I wonder what version

[gmx-users] polymer chain length and density

Dear experts, I have a quick and naive inquiry. I see in the molecular dynamics simulations that density of the polymers increase slightly with increasing degree of polymerization ( or Mw). Even for the systems having the same total atom numbers but one with less number of chains of higher Mw. My

Re: [gmx-users] polymer chain length and density

On 27/10/2011 10:43 AM, Juliette N. wrote: Dear experts, I have a quick and naive inquiry. I see in the molecular dynamics simulations that density of the polymers increase slightly with increasing degree of polymerization ( or Mw). Even for the systems having the same total atom numbers but

[gmx-users] Re:polymer chain length and density

Dear experts, I have a quick and naive inquiry. I see in the molecular dynamics simulations that density of the polymers increase slightly with increasing degree of polymerization ( or Mw). Even for the systems having the same total atom numbers but one with less number of chains of higher

[gmx-users] convert parameters of Buckingham potential to/from LJ potential

Dear gmx Users, I am trying to convert parameters of Buckingham potential to/from LJ potential. It seems that there is tool in Gromacs, g_sigeps which is capable of doing this. However,when I typed the following command: ./sigeps_mpi -nice 2 -A 6159492 -B 0.019891 -C 0.002692 -qi -1.041094 -qj

Re: [gmx-users] convert parameters of Buckingham potential to/from LJ potential

Kan wrote: Dear gmx Users, I am trying to convert parameters of Buckingham potential to/from LJ potential. It seems that there is tool in Gromacs, g_sigeps which is capable of doing this. However,when I typed the following command: ./sigeps_mpi -nice 2 -A 6159492 -B 0.019891 -C 0.002692

Re: [gmx-users] position restrained minimization on the one part of a system

Hi Atila, ; Include chain topologies #include complex_Protein_chain_A.itp #include complex_DNA_chain_B.itp ; Include Position restraint file #ifdef POSRES #include posre_Protein_chain_A.itp ; Include Position restraint file #ifdef POSRES #include posre_Protein_chain_B.itp Aside from