[gmx-users] Re: gb_saltconc in implicit water simulations
Can anyone answer this question or guide me somewhere with helpful information? Thanks, Bob On Thu, Dec 9, 2010 at 4:52 PM, Bob Johnson wrote: > Hello everyone, > I am trying to use implicit solvent with a CG DNA model. The model, > however, uses explicit charges, which means that the DNA carries an overall > negative charge. When using implicit solvent with a charged system in other > codes (e.g. Amber), the electrolyte is taken care of implicitly as well. > However, in Gromacs this is currently not implemented since gb_saltconc is > always set to 0. Without any salt, the DNA duplex is obviously unstable. Are > there plans on implementing implicit counterions so that one can set > gb_saltconc to nonzero values? > > It doesn't seem natural to include explicit counterions to neutralize the > system when using implicit solvent. Is there a typical protocol one follows > to neutralize charged systems when using implicit solvent? > Thanks, > Bob > > -- > Bob Johnson, PhD > Institute for Computational Molecular Science > Temple University > 1900 North 12th Street > Philadelphia, PA 19122 > http://astro.temple.edu/~rjohnson <http://astro.temple.edu/%7Erjohnson> > -- Bob Johnson, PhD Institute for Computational Molecular Science Temple University 1900 North 12th Street Philadelphia, PA 19122 http://astro.temple.edu/~rjohnson -- 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 (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gb_saltconc in implicit water simulations
Hello everyone, I am trying to use implicit solvent with a CG DNA model. The model, however, uses explicit charges, which means that the DNA carries an overall negative charge. When using implicit solvent with a charged system in other codes (e.g. Amber), the electrolyte is taken care of implicitly as well. However, in Gromacs this is currently not implemented since gb_saltconc is always set to 0. Without any salt, the DNA duplex is obviously unstable. Are there plans on implementing implicit counterions so that one can set gb_saltconc to nonzero values? It doesn't seem natural to include explicit counterions to neutralize the system when using implicit solvent. Is there a typical protocol one follows to neutralize charged systems when using implicit solvent? Thanks, Bob -- Bob Johnson, PhD Institute for Computational Molecular Science Temple University 1900 North 12th Street Philadelphia, PA 19122 http://astro.temple.edu/~rjohnson -- 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 (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Negative number of RMSD calculations left in g_cluster
Hello everyone, I am attempting to use g_cluster on a large data set (about 69000) frames. I'm on a machine that has 48 GB of RAM, so I shouldn't be running out of memory. As g_cluster runs, it counts down the number of RMSD calculations left. Normally this number is positive (as it should be). Instead of stopping at 0, however, the calculation keeps on going and displays a negative number of RMSD calculations that remain. This negative keeps on getting more and more negative until eventually the machine runs out of memory and I get a seg fault. I have run this same exact calculation skip 2 (35000 frames instead of 69000) and it works fine. What is the reason for the negative number of RMSD calculations and how can it be fixed? Thanks, Bob -- Bob Johnson, PhD Institute for Computational Molecular Science Temple University 1900 North 12th Street Philadelphia, PA 19122 http://astro.temple.edu/~rjohnson -- 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 the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Columns in log file of g_cluster
Hello everyone, What do columns 3 and 5 (the rmsd numbers next to the number of structures in the cluster and the frame number of the central cluster, respectively) indicate in the log file of g_cluster? Thanks, Bob -- 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 the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PMF using umbrella sampling
Can you use runtype=constraint in parallel? I switched to using runtype=umbrella because I received error messages that the constraints can't be run in parallel. Also...yes...I switched up angstroms and nanometers...I don't know how many times I've made that mistake and couldn't find it myself... Thanks, Bob On Tue, Sep 1, 2009 at 2:34 AM, Berk Hess wrote: > Hi, > > Firstly, you are not constraining (runtype=constraint), but using a harmonic > umbrella potential. > > Secondly, your distance of 28.9 nm seems enormous, maybe you mixed > up nanometers and Angstroms here? > > Thirdly, I would strongly suggest to switch to Gromacs 4.0.5. > I have completely rewritten the pull code for Gromacs 4 > and things now work much easier and better. > > Berk > >> Date: Mon, 31 Aug 2009 12:18:06 -0500 >> From: bobjohnson1...@gmail.com >> To: gmx-users@gromacs.org >> Subject: [gmx-users] PMF using umbrella sampling >> >> Hello everyone, >> I'm trying to compute the PMF for pulling two proteins apart. I'm >> planning on setting up several runs where the COM separation of the >> proteins is constrained and the constraint force is measured over the >> course of a long simulation. However, I'm having trouble doing this >> because I'm unsure of the inputs in the .ppa file. I'm trying to do >> this with Gromacs 3.3.3. Here is the .ppa file I'm using: >> >> runtype = umbrella >> ngroups = 1 >> reference_group = knob >> reftype = com >> pulldim = Y Y Y >> group_1 = car >> k1 = 1000 >> pos1 = 0.0 0.0 28.8989219666 >> >> Here, there are two proteins: car and knob. The COM of car is located >> at (0.0 0.0 28.8989219666) relative to knob. The problem I'm >> experiencing is that the simulation results in the two proteins being >> pulled apart instead of constrained at distance pos1. I believe that >> I'm misinterpreting the inputs. Does anyone know the solution? >> Thanks, >> Bob >> ___ >> gmx-users mailing list gmx-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 the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > What can you do with the new Windows Live? Find out > ___ > 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 the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Bob Johnson, PhD Institute for Computational Molecular Science Temple University 1900 North 12th Street Philadelphia, PA 19122 http://www.sas.upenn.edu/~robertjo ___ 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 the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PMF using umbrella sampling
Hello everyone, I'm trying to compute the PMF for pulling two proteins apart. I'm planning on setting up several runs where the COM separation of the proteins is constrained and the constraint force is measured over the course of a long simulation. However, I'm having trouble doing this because I'm unsure of the inputs in the .ppa file. I'm trying to do this with Gromacs 3.3.3. Here is the .ppa file I'm using: runtype = umbrella ngroups = 1 reference_group = knob reftype = com pulldim = Y Y Y group_1 = car k1 = 1000 pos1 = 0.0 0.0 28.8989219666 Here, there are two proteins: car and knob. The COM of car is located at (0.0 0.0 28.8989219666) relative to knob. The problem I'm experiencing is that the simulation results in the two proteins being pulled apart instead of constrained at distance pos1. I believe that I'm misinterpreting the inputs. Does anyone know the solution? Thanks, Bob ___ 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 the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Launching Replica Exchange MD
Hello everyone, I can't seem to find how to start a replica exchange MD job. I have a separate .tpr file for each replica. How do I give these to mdrun? Also, for debugging purposes I wanted to run a few of my replicas on the same node (otherwise I have to wait in a queue) just to make sure my acceptance ratio is what I think it should be. Is this possible? Thanks, Bob ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] x2top stalls when generating topology file
Hello everyone, There has been other reports on the mailing list where users attempt to generate a topology with x2top only to have the program stall and generate no output. I'm using x2top (from Gromacs version 3.3.1) to generate topology files for infinite carbon nanotubes and graphene sheets. Starting from a pdb file with box dimensions compatible with PBC I enter: x2top -f .pdb -o .top -pbc I then select force field 7 (the deprecated Gromacs force field) and I get the following output: Looking whether force field file ffgmx.rtp exists Opening library file /home/bob/programs/gromacs/share/gromacs/top/ffgmx.rtp Generating bonds from distances... Opening library file /home/bob/programs/gromacs/share/gromacs/top/ffgmx.atp There are 53 type to mass translations atom 0 At this point the program just sits there while still occupying 100% of the CPU. I don't experience this problem when using x2top from version 3.3 that was compiled on a different machine. Does anyone know the fix to this problem? Maybe it has to do with the way the code is compiled? Thanks, Bob ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Calculation of Electrostatic Potential at a Nanotube
Hello everyone, I am trying to calculate the electrostatic potential at the surface of a carbon nanotube from an MD simulation involving water and other adsorbates binding to the nanotube. Since the nanotube atoms are uncharged this is how I was proceeding: 1. I computed the trajectory using the normal force fields 2. I then went and altered the nanotube topology file and gave each carbon atom a fictitious charge of 0.1 3. I then used the rerun feature to recalculate the electrostatic energy between the nanotube and water (for example) 4. The average electrostatic potential is this energy divided by the total nanotube charge However, it seems that my results (e.g. the sign of the potential) does not agree with some preliminary calculations I did where I calculate the potential via brute force summing q/r. One thing that I'm concerned about is that the total charge of my system when I use mdrun -rerun is non-zero since I'm giving the nanotube atoms a charge. Will this effect the calculated electrostatic energy? Thanks, Bob ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] File input/output error: Can not determine precision of trn file
Hello everyone, It seems that one of my trajectory files has an error. I get the following message when using trjconv -f trajectory.trr. File input/output error: Can not determine precision of trn file I noticed that there was a previous question about this error message. However, the only available workaround pertained to trajectories saved in xtc format. Has there be any new developments for the trr format? Thanks, Bob ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Measuring dihedral energy of various selections
Hello everyone, I would like to measure the dihedral energy of certain portions of the same molecule over the course of a previously calculated trajectory. It's important that I get the energy of ONLY these portions. I thought of saving the trajectory of the portion in interest using trjconv. Then using mdrun -rerun to calculate the dihedral energy of this portion. However, this won't work because I would have to make a topology file that contains ONLY this portion. Any ideas? Bob ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Generating a PQR file
Hello everyone, I would like to create a PQR file (basically a PDB file but with charges in B-field and radii in occupancy field). However, there doesn't seem to be any straightforward way to do this. I noticed that this could be done with editconf, however this is difficult given the way I have my topologies set up. I have a separate topology (.itp) for each molecule in my system (dna, water, counterions, etc.). Thus, the atom numbers in these files are not unique. Thus, there is no good way of feeding in the charges to editconf by listing the charge for each atom number. Is there a way to extract this information from a .tpr file? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] AFM Pulling Rate
Hello everyone, I am using AFM pulling to drag a dna base across the surface of a graphene. I'm doing this in vaccuum. It seems that the base is pulled at the same rate no matter what value I specify in afm_rate1. Here is my pull.ppa file: runtype = afm group_1 = ssdna-ions pulldim = N N Y afm_rate1 = 0.05 afm_k1 = 100 afm_dir1 = 0 0 1 I'm using version 3.3. Does anyone know what's going on? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_dipoles -slab option
Hello everyone,
Water tends to align at a hydrophobic surface in a way to maximize H-bonds.
Doing this leads to a dipole moment that is perpendicular to the surface
(pointing away from the surface). Is this correct?
I'm trying to verify this with a simulation. I have an uncharged surface in the
xz-plane. I'm using g_dipoles with the -slab option to get the dipole moment of
water slabs in the y direction. Below is the output. There are 5 columns of data
for some reason and I can't interepret it. The first column is the position of
the water slab. I can only assume that column 2 is the dipole in the x
direction and column 3 is the dipole in the y direction and so on. Is that
correct? What is the last column for?
@title "Average dipole moment per slab"
@xaxis label "Box-Y (nm)"
@yaxis label "\f{12}m\f{4} (D)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "\f{12}m\f{4}\sX\N"
@ s1 legend "\f{12}m\f{4}\sY\N"
@ s2 legend "\f{12}m\f{4}\sZ\N"
0.500 0.000 0.000 0.000 0.000
1.500 -46.367 3.869 41.074 62.064
2.500 36.106 0.765 3.870 36.321
3.500 7.638 0.371 1.223 7.744
4.500 -18.688 1.380 -20.000 27.406
5.500 8.237 4.201 -9.015 12.914
6.500 -0.103 0.057 -0.023 0.119
7.500 0.000 0.000 0.000 0.000
8.500 0.000 0.000 0.000 0.000
9.500 0.000 0.000 0.000 0.000
Thanks,
Bob Johnson
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[gmx-users] Energy Group Exclusions
Hello everyone, I'm simulating a nanotube on a substrate. My substrate is just a simple impenetrable wall of closely packed atoms. To restrict the substrate to a planar geometry I am using position restraints on substrate atoms as well as using energy group exclusions (energygrp_exl = substrate substrate) in my input file. I get the following warning upon running grompp. WARNING: Can not exclude the lattice Coulomb energy between energy groups The substrate atoms are uncharged and only have the C12 value defined in my topology file. Is this warning generated by default when using any kind of energy group exclusions whatsoever? It's obvious to me that if my substrate were charged it would also contribute to the PME calculation. Thus, the Coulomb energy of the substrate would be impossible to get rid of. Is my thinking correct? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Simulating a substrate
Hello everyone, I would like to simulate a carbon nanotube on a substrate. My idea is to make a 2D monolayer of closely spaced atoms that make an impenetrable wall. I will then restrain the positions of these atoms. I will then place the nanotube on top of it. However, I'm not quite sure what LJ parameters I should use for the substrate. Any ideas? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Huge fluctuations for pressure coupling
Hello everyone, I have a 20 base single stranded DNA with counterions that is hydrated with about 9000 water molecules. My pressure coupling input looks like this: pcoupl = Parrinello-Rahman pcoupltype = isotropic ref_p = 1.01 compressibility = 4.5e-5 tau_p = 1.0 However, I get huge pressure fluctuations (RMS fluctuation of 1.71704e+02) and it seems that the coupling doesn't even enforce the correct pressure (average pressure of 1.68282e-01). I didn't see anyone in the mailing list that had a similar problem. Does anyone know what's going on? Thanks, Bob ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Implementing Radial Distance Constraints
>please be more clear. > >if we assume your cnt is centered along the z-axis, given roughly by >x^2+y^2 = d0. Am I correct in assuming that you want all other particles >to have x^2+y^2 <= d1, where d1 < d0 ? > >-- >David. The molecules in my system adsorb to the tube's outer wall. They are not inside the tube. Typically, the adsorbates reside 3.5A above the nanotubes surface (a typical distance for molecules interacting via VdW with an aromatic molecule). I want to constrain molecules to always adopt a monolayer about the nanotube. Therefore, I want to put a constraint on certain atoms to reside 3.5A above the nanotube. Let's say my nanotube has a radius of 0.5A. I would then want to implement a potential given by V = 1/2 k (R-0.5A)^2 where R = sqrt(x^2+y^2). This way, the atoms are able to slide along the z and cirumferential directions. Bob ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Implementing Radial Distance Constraints
Hello everyone, My system consists of a carbon nanotube and various chemicals that adsorb to the tube. I would like to use radial distance constraints to enforce adsorbates to maintain a fixed distance away from the nanotube. These restraints must obey the relation R = sqrt (x^2 + y^2) = user defined constant. With this type of restraint the adsorbates are free to move along the z and circumferential directions (something that can not be done with normal position or distance restraints). I would like to add a restraint potential given by V = 1/2*k*(R-R0)^2 = 1/2*k*( sqrt(x^2+y^2) - R0)^2. Here R0 is the fixed radial distance. Is this difficult to implement in Gromacs? What file in the source code would I edit? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Radial distance restraints
Hello everyone, Is there any way to use radial distance restraints? For example, my system is cylindrically symmetric (it's a carbon nanotube) and I would like to restrain molecules to a certain distance away from the nanotube axis. Obviously, I don't care if they the slide along the z-axis or change their orientation with respect to the nanotube surface. That is why only radial constraints (sqrt(x^2 + y^2) = constant) will work. Any way to do this? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Orientation restraints
Hello everyone, My system consists of DNA and a carbon nanotube. I would like to restrain the DNA bases in a way that the plane formed by each base is parallel to the z-axis. In other words, I would like to orient the bases such that the normal of each plane is perpendicular to the z-axis. I don't think using angle restraints is sufficient for what I want to do because there you can only restrain pairs of atoms. Any ideas how I could define a normal vector to each plane and have that maintain a 90 degree angle with respect to the z-axis? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Non-zero system charge
Hello everyone, I am using PME to handle electrostatics. What happens if I run a simulation with a non-zero net charge? Does GROMACS automatically provide some sort of background charge to neutralize the system? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Restarting a periodic simulated annealing run
Hello everyone, Is there a way to restart a periodic annealing run if the previous run stops in the middle? For example, if I'm annealing periodically between 500K and 300K and the simulation stops at, say, 400K, is there a way to restart the simulation so that the temperature ramp starts at 400K and proceeds in the same direction as when it ended? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Dummy atoms for electrostatics calculation
Hello everyone, My system consists of a single stranded DNA adsorbed on a carbon nanotube. I would like to calculate the electrostatic potential at the surface of the nanotube due to DNA, water and counterions. Right now, each nanotube atom has a charge of 0. What I would like to do is the following: 1) Assign a small identical charge (+0.001 say) to each nanotube atom 2) Run MD and calculate the Coulombic energy between the nanotube and the environment 3) The average potential that the nanotube sees is then this energy divided by the total nanotube charge The only problem with this is I do not want the nanotube charges to affect the dynamics of the molecules in the environment. In other words, I want the DNA, water, counterions to see an uncharged nanotube for the purpose of calculating the trajectories. Is there any way to do this with dummy atoms? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
