Re: [gmx-users] RMS deviation after position restraint dynamics

sukesh chandra gain wrote: Dear All, I am running position restraint dynamics to restrain the atom positions of the protein to restrict their movement in the simulation. Then, how could there be any RMS deviation for the protein before and after the position restraint dynamics run? (Although t

Re: [gmx-users] RMS deviation after position restraint dynamics

A restraint is not a constraint, and assuming that you are simulating your system at a finite temperature, you should expect to see some fluctuations in a given atom's position. Josh On May 17, 2009, at 11:47 PM, sukesh chandra gain wrote: Dear All, I am running position restraint dynamic

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests that you'd have to look for an increase in volume. But how to do that, how to define the volume of the protein is still a matter of setting your criteria and finding the right tools to assess

[gmx-users] g_rdf -xy

Dear gmx-users, I simulate a vapor/water/decane/vapor interface system. The interface is xy plane. I want to analysis water structure at the interface using g_rdf program along z axis with -xy parameter. But the calculation is hanged as the following: Select a reference group and 1 group Group

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar > Hi, > > Well, I think 'swelling' is unambiguously, though roughly, defined as > 'growing larger', which suggests that you'd have to look for an > increase in volume. But how to do that, how to define the volume of > the protei

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

stretching != swelling, e.g. On Mon, May 18, 2009 at 10:46 AM, Bhanu wrote: > How about checking radius of gyration??? > > 2009/5/18 Tsjerk Wassenaar >> >> Hi, >> >> Well, I think 'swelling' is unambiguously, though roughly, defined as >> 'growing larger', which suggests that you'd have to look

RE: [gmx-users] Constraints specified in .mdp as well as in .top files

Hi, I think the manual is pretty clear on this: constraints: none No constraints except for those defined explicitly in the topology, i.e. bonds are represented by a harmonic (or other) potential or a Morse potential (depending on the setting of morse) and angles by a harmonic (or other) potenti

RE: [gmx-users] g_rdf -xy

Hi, g_rdf -xy does not do what you want. It determines rdf's using only the x and y components of the distance and averages over z. g_rdf hangs probably because you use -nbin 100, which sets bins with a width of 100 nm (and not 100 bins as you probably thought). There is currently no Gromacs to

Re: [gmx-users] adding non-polar hydrogens - incompatibility of pdb2gmx and grompp

Protonate does the job of adding all of the hydrogens but non-polar hydrogens are not recognised by pdb2gmx so that the topology file isn't created. Apparently grompp needs the *.top file in input (It says "Input/Output error upon giving only the *.gro file in input). Does this mean that I can't

[gmx-users] g_rdf -xy

Dear Berk, I am sorry that I have a mistake in the first letter. In fact I used -bin 0.05, not 100. Yet the result is hanged. Maybe as you said, the current Gromacs can not realize what I want to do. Thanks again! H.Y. Xiao ___ gmx-users mailing

[gmx-users] Input/Output error using grompp

Hello, I can't get rid of an error occurring using grommp: --- Program grompp, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: grompp.mdp --- my command line is: >> grompp -r 4AKEpolHsol.gro -4AKEpolH.t

Re: [gmx-users] Input/Output error using grompp

Stefano Meliga wrote: Hello, I can't get rid of an error occurring using grommp: --- Program grompp, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: grompp.mdp --- my command line is: >> grompp -r 4AK

[gmx-users] mdp file for local pressure

Dear sir, I am calculating local pressure by gromacs-localp. My .mdp file is following integrator = sd ; stochastic dynamics -> Langevin! ld_seed = -1 ; random seed for sd dt = 0.002 ; ps ! nsteps

Re: [gmx-users] Input/Output error using grompp

Am 18.05.2009 um 13:26 schrieb Stefano Meliga: my command line is: >> grompp -r 4AKEpolHsol.gro -4AKEpolH.top -o 4AKEpolH.tpr -po 4AKEpolH.mdp what's your 2nd argument? the grompp.mdp is afaik mandatory - you can just create an empty one before, e.g. if you grompp for genion... touch

Re: [gmx-users] adding non-polar hydrogens - incompatibility of pdb2gmx and grompp

Stefano Meliga wrote: Protonate does the job of adding all of the hydrogens but non-polar hydrogens are not recognised by pdb2gmx so that the topology file isn't created. Apparently grompp needs the *.top file in input (It says "Input/Output error upon giving only the *.gro file in input). Do

Re: [gmx-users] adding non-polar hydrogens - incompatibility of pdb2gmx and grompp

Stefano Meliga wrote: Protonate does the job of adding all of the hydrogens but non-polar hydrogens are not recognised by pdb2gmx so that the topology file isn't created. Thus you've discovered that pdb2gmx isn't magic. It can only create topologies whose building blocks are already defined i

Re: [gmx-users] positions and velocities of COM of whole water molecules instead of those of individual atoms?

>> Dear GROMACS Masters, >> >> is there a trick to obtain coordinates and velocities of center of >> mass of each water molecule? >> > > Have a look at g_traj, although to analyze each molecule separately could > take many iterations with specific index groups. > g_traj can really do it (for coordi

Re: [gmx-users] Re: parameter of RB potential for OPLS force field

Dear Justin: Thanks for your response. I saw this in the ffoplsaabon.itp, which I think is a Periodic potential. [ dihedraltypes ] ; ijkl func coefficients ; Added DvdS for Quartz simulations SI OS1 0.000 3.766 3 SI OH1 0.000 3.766

[gmx-users] how to add shear force in gromacs

Hi all users, I just wonder how I can add the shear force in gromacs. I have checked the manual but failed to find some effective ways to do that. Any suggestions will be highly appreciated. Thank you very much. Yang ___ gmx-users mailing listg

[gmx-users] shift function for vdwtype and density

Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift for vdwtype? -- Yanmei Song Ph.D.

Re: [gmx-users] Re: parameter of RB potential for OPLS force field

Yanmei Song wrote: Dear Justin: Thanks for your response. I saw this in the ffoplsaabon.itp, which I think is a Periodic potential. So check out table 5.4 in the manual and find out for sure! [ dihedraltypes ] ; ijkl func coefficients ; Added DvdS for Quartz simulations

Re: [gmx-users] shift function for vdwtype and density

Yanmei Song wrote: Dear All: I found when I changed the vdwtype from cut-off to shift, the density of the system decrease significantly.All the other setting in the mdp file remain unchanged. For example the density of TIP5P water drops to 962. Does it mean I can not use the shift for vdwtype

Re: [gmx-users] shift function for vdwtype and density

Dear Mark: Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from the literature value of 982.

Re: [gmx-users] shift function for vdwtype and density

Yanmei Song wrote: Dear Mark: Thanks for your answer. I have to use the same mdp file for both water and another polymer molecules in my system, right? Then if the shift function works well for the polymer, I can not get the best result for TIP5P? The density of TIP5P is different from th

[gmx-users] Re: Molecule Jumps

Hi All, I just wanted to let you know how I resolved my problem, in case anyone else experiences a similar problem in the future. My structure spanned all four quadrants around the origin (i.e. the 4 vertices of my structure were (-x, -y), (-x,y), (x,-y), & (x,y)). I think because it spanned all

Re: [gmx-users] shift function for vdwtype and density

Dear Justin: Yes. Before I do the water+polymer, I did both the bulk systems separately. The density of TIP5P I mentioned earlier is the results for pure water bulk system. My concern is that if it is reasonable that the property of the system changes with different mdp conditions? Since when I di

Re: [gmx-users] shift function for vdwtype and density

Yanmei Song wrote: Dear Justin: Yes. Before I do the water+polymer, I did both the bulk systems separately. The density of TIP5P I mentioned earlier is the results for pure water bulk system. My concern is that if it is reasonable that the property of the system changes with different mdp

Re: [gmx-users] shift function for vdwtype and density

Dear Justin: Yes and I tried dispersion correction and it gives a larger density than I expected. The density of the polymer by vdwtype=shift is more close to the experimental value. Then your suggestion would be to choose the vdwtype=cut-off under this condition even if it result in larger densi

Re: [gmx-users] shift function for vdwtype and density

Yanmei Song wrote: Dear Justin: Yes and I tried dispersion correction and it gives a larger density than I expected. The density of the polymer by vdwtype=shift is more close to the experimental value. Then your suggestion would be to choose the vdwtype=cut-off under this condition even if

Re: [gmx-users] shift function for vdwtype and density

Perhaps I can contribute something else that might be a bit more useful. It just occurred to me that if you are only changing the vdwtype parameter, then you are not correctly implementing the shift function. See here for proper use of a shift potential: http://www.gromacs.org/documentatio

RE: [gmx-users] mdp file for local pressure

The error message explicitly tells you what is wrong: "Expected 2 elements for wall_atomtype, found 0" And looking in your .mdp file ... ;WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpo

Re: [gmx-users] Re: Molecule Jumps

darre...@ece.ubc.ca wrote: Hi All, I just wanted to let you know how I resolved my problem, in case anyone else experiences a similar problem in the future. My structure spanned all four quadrants around the origin (i.e. the 4 vertices of my structure were (-x, -y), (-x,y), (x,-y), & (x,y)). I t

Re: [gmx-users] shift function for vdwtype and density

Dear Justin: Thanks so much for your effort and information. Perhaps I did not set the proper value for vdw_switch. I will try some value. I really appreciate your nice help! On Mon, May 18, 2009 at 5:24 PM, Justin A. Lemkul wrote: > > Perhaps I can contribute something else that might be a bit

Re: [gmx-users] shift function for vdwtype and density

Justin A. Lemkul wrote: Yanmei Song wrote: Dear Justin: Yes and I tried dispersion correction and it gives a larger density than I expected. The density of the polymer by vdwtype=shift is more close to the experimental value. Then your suggestion would be to choose the vdwtype=cut-off und

[gmx-users] Has anyone adapted an Allinger force field for GROMACS? (MM,MM+,MM2,MM3...)

Good morning! I would like to use one of the MM force fields (originally by Allinger) in GROMACS. Has anyone tried to adapt such a force field? I know of at least two previous inquiries: Corina Barbu in 2003: http://www.gromacs.org/pipermail/gmx-users/2003-October Konrad Piwowarczyk in 2004

Re: [gmx-users] Has anyone adapted an Allinger force field for GROMACS? (MM,MM+,MM2,MM3...)

Inon Sharony wrote: Good morning! I would like to use one of the MM force fields (originally by Allinger) in GROMACS. Has anyone tried to adapt such a force field? Short answer: No. It should not be too hard if you want to try (that is if the functional form is implemented already).