[gmx-users] Unexpected behavior of g_msd

Dear GROMACS-ites, I am a little confused by the behavior of g_msd. I have a trr file with data points from t=0 to t=100 ps and thought that the following command would perform a regression for the data points between t=60 ps and t=100 ps to determine the diffision constant of the ammonia gas i

Re: [gmx-users] Re: How to make carbon nanotube infinite?

Justin A. Lemkul wrote: NOTE 2 [file em.mdp, line unknown]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. I also just noticed that you have not specified "periodic_molecules = yes" in the .mdp file. This is

[gmx-users] Re: How to make carbon nanotube infinite?

Cun Zhang wrote: I hope generate sharing bonds between the atoms at the top edge and the atoms at the bottom edge of CNT by x2top. But the parameter -pbc does not work. So I add 4 layers at the top of CNT.pdb and rename it CNT_new.pdb, that is, the front 832 rows of them are same. The

[gmx-users] Re: How to make carbon nanotube infinite?

Thank you, Justin ! I have add the output generated by grompp and mdrun at the end. > Cun Zhang wrote: > > hi, Justin. Thank you for your patience ! > > > > I'm still in trouble with infinite CNT simulation. > > > > I'm trying to simulate the interaction of a infinite (16,0) CNT(CNT_A) > > wit

Re: [gmx-users] Continue simulation

I got it now. Thanks. Happy TG! tpbconv -s md.tpr -extend 1 -o next.tpr mdrun -s next.tpr -cpi md.cpt Checkpoint file is from part 1, new output files will be suffixed part0002. Reading file next.tpr, VERSION 4.0.5 (single precision) Reading checkpoint file md.cpt generated: Tue Nov 24 15:00:12 2

Re: [gmx-users] Continue simulation

Jack Shultz wrote: Is it ok just to use tpbconv, even though we get this message "Continuation should be done by loading a checkpoint file with mdrun -cpi"? Please see the last paragraph in the "Version 4" section here: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations ++

Re: [gmx-users] Continue simulation

Jack Shultz wrote: Is it ok just to use tpbconv, even though we get this message "Continuation should be done by loading a checkpoint file with mdrun -cpi"? It depends on your objective, and you haven't told us enough about your .tpr and why your simulation stopped for us to know. See http://

Re: [gmx-users] Coulomb Interactions

nishap.pa...@utoronto.ca wrote: Hi! Does anyone know how I can turn off the coulomb interactions in the .mdp file? I tried to change the values of rcoulomb to 0, but it doesn't work. There's no ready way to do this and it's normally not a sensible thing to do. Zeroing the charges in the .top

[gmx-users] Continue simulation

Is it ok just to use tpbconv, even though we get this message "Continuation should be done by loading a checkpoint file with mdrun -cpi"? ++ I have tried mdrun using the -cpi flag mdrun -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md Then when I run the next u

[gmx-users] Coulomb Interactions

Hi! Does anyone know how I can turn off the coulomb interactions in the .mdp file? I tried to change the values of rcoulomb to 0, but it doesn't work. Thanks NP -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: [gmx-users] Genbox

Lum Nforbi wrote: Hello all, How long does it usually take genbox to run? Generally, a few seconds, but that will depend on the size of your system and what you're trying to do (simple solvation, molecule insertion, etc). It is not possible to say for certain, since processor speed an

[gmx-users] Genbox

Hello all, How long does it usually take genbox to run? Thanks, Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to th

Re: [gmx-users] Group Cl not found in indexfile

SHANG Yuan wrote: Hi,gmx-users, I'm following Kerrigan's "GROMACS Tutorial for Drug-Enzyme Complex", but encounter with some problems（my GMX version is 4.0）. firstly, after "genion -s trp_b4ion.tpr -o trp_b4em.gro -nname Cl -nn 9" command, I add "Cl 9" at the end of "trp.top" file, and the

[gmx-users] Group Cl not found in indexfile

Hi,gmx-users, I'm following Kerrigan's "GROMACS Tutorial for Drug-Enzyme Complex", but encounter with some problems（my GMX version is 4.0）. firstly, after "genion -s trp_b4ion.tpr -o trp_b4em.gro -nname Cl -nn 9" command, I add "Cl 9" at the end of "trp.top" file, and the following "grompp" com

Re: [gmx-users] Normalization in g_rdf

Ah, now I see what you meant. Then it is fine. That is a separate issue and is not really a problem for me. Thank you, Ondrej On Tue, Nov 24, 2009 at 17:39, Berk Hess wrote: > Hi, > > Sure g_rdf takes care of pressure coupling, but the cut-off of the rdf plot > is set from the initial frame. >

RE: [gmx-users] Normalization in g_rdf

Hi, Sure g_rdf takes care of pressure coupling, but the cut-off of the rdf plot is set from the initial frame. So if your volume fluctuates a lot, you might have incorrect normalization very close to the cut-off. But in "normal" liquid simulations the box length will never change more than 1%.

Re: [gmx-users] How to make carbon nanotube infinite?

Cun Zhang wrote: hi, Justin. Thank you for your patience ! I'm still in trouble with infinite CNT simulation. I'm trying to simulate the interaction of a infinite (16,0) CNT(CNT_A) with 832 atoms and water. I'm using x2top to generate the CNT.itp with share-bonds. The idea is that I genera

Re: [gmx-users] Normalization in g_rdf

Hi again, I thought pressure coupling is handled by g_rdf. Looking at the code, it seems that the block starting with: /* Must init pbc every step because of pressure coupling */ takes care of that, so even with a relatively big volume change at the beginning, it should not be a problem. Is

RE: [gmx-users] Normalization in g_rdf

Hi, g_rdf limits the distance to half the minimum periodic image distance. So the volume normalization is always simply 4 pi r^2. It uses the starting unit-cell with a factor of 0.99. So you would only see strange effects when the box length reduces more than 1% due to pressure coupling. Berk

Re: [gmx-users] How to make carbon nanotube infinite?

hi, Justin. Thank you for your patience ! I'm still in trouble with infinite CNT simulation. I'm trying to simulate the interaction of a infinite (16,0) CNT(CNT_A) with 832 atoms and water. I'm using x2top to generate the CNT.itp with share-bonds. The idea is that I generate a (16,0) CNT(CNT_B)

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

On Tue, 24 Nov 2009, lammps lammps wrote: 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

Re: [gmx-users] Normalization in g_rdf

On Tue, Nov 24, 2009 at 11:12, Berk Hess wrote: > Hi, > > If you have N molecules with total volume which is significantly less than > the unit-cell, > as is the case for ions in solvent, the RDF of the N molecules againt > themselves > will converge to (N-1)/N. > > Berk Hi, thanks for the remin

Re: [gmx-users] Normalization in g_rdf

On Tue, Nov 24, 2009 at 13:01, Omer Markovitch wrote: > > On Tue, Nov 24, 2009 at 02:27, Ondrej Marsalek > wrote: >> >> Dear all, >> >> I would like to understand better the way g_rdf performs >> normalization. I have two unexpected results: >> >> 1) In a simple simulation of atomic ions in water

Re: [gmx-users] g_msd => The MSD and periodic boundary condition

On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin wrote: > So, how can I remove the periodic boundary condition to get the truly > movement of the atoms between the two time steps ? > Removing PBC and placing atoms back into their "true" location is easy. In general, if an atom has moved more than ha

Re: [gmx-users] Normalization in g_rdf

On Tue, Nov 24, 2009 at 02:27, Ondrej Marsalek wrote: > Dear all, > > I would like to understand better the way g_rdf performs > normalization. I have two unexpected results: > > 1) In a simple simulation of atomic ions in water in a cubic box, I > get RDFs that clearly reach a constant value at l

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

delta G = -R*T*ln(K). Now its just a matter of describing your hbond cleavage reaction. For water, the reaction is usualy bonded<-->nonbonded, and a geometrical criteria is usualy applied. Take a look for example at this paper: "The Distribution of Acceptor and Donor Hydrogen Bonds in Bulk Liquid W

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

lammps lammps wrote: 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? First, you have to define the energy change :-) Th

[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 -- wende -- gmx-

RE: [gmx-users] Normalization in g_rdf

Hi, If you have N molecules with total volume which is significantly less than the unit-cell, as is the case for ions in solvent, the RDF of the N molecules againt themselves will converge to (N-1)/N. Berk > Date: Tue, 24 Nov 2009 01:27:27 +0100 > From: ondrej.marsa...@gmail.com > To: gmx-user