[gmx-users] Looking for advice on Monte Carlo simulations, please

are spending lots of time and resources to continually add features! I am not yet very fluent in C/C++ and am not much of a programmer. I am more of a chemist/simulator. So I just want to thank you all for all your work on making Gromacs what it is! Thanks! Andrew DeYoung Carnegie Mellon

[gmx-users] Conceptual question about the computational scaling of MD

computationally expensive part of MD. Is it thus reasonable to say that MD overall scales as O(N logN)? Or does MD overall scale in some other way? I have been having difficulty finding a textbook or paper that states or estimates the scaling of MD. Thank you so much for your time! Andrew

[gmx-users] Re: mdrun-gpu error message on Gromacs 4.5.5

much for your help! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] mdrun-gpu error message on Gromacs 4.5.5

or previously discussed on this mailing list. Does this error message suggest that I am calling mdrun-gpu incorrectly, or that OpenMM is improperly installed? Thank you kindly for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Including polarizability by a Drude oscillator or the shell model

, I do not see in the manual where the use of the shell model in Gromacs simulations is described. Do you know if some sort of tutorial exists about the use of the shell model (or the Drude oscillator) in Gromacs? Thank you so much for your time! Andrew DeYoung Carnegie Mellon University -- gmx

[gmx-users] General conceptual question about advantage of GPUs

is typical. (I would not expect it for Gromacs, though, since Gromacs is already super fast!) If you have time, do you know of any review or opinion papers that might discuss the advantages (advantages of performance or otherwise) of using GPUs over CPUs? Thanks for your time! Andrew DeYoung

[gmx-users] Re: General conceptual question about advantage of GPUs

Thank you, Justin. This is very helpful to me, especially the link to the GPU conference, which I think will be very helpful. I have done a little benchmarking on our ~7000 atom system, and in those tests the scaling was excellent -- almost linear when comparing 4, 8, 12, 16, 24 CPUs. I am

[gmx-users] Re: What is the purpose of the [ pairs ] section?

atomtypes (two different carbon atomtypes, one oxygen atomtype, and one hydrogen atomtype). Does anyone have any thoughts on this? Thank you so much for all of your EXTREMELY helpful explanations, everyone! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Re: What is the purpose of the [ pairs ] section?

nonbonded interactions are considered? If so, why is this the case if I have set gen-pairs = yes? Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org

[gmx-users] Re: What is the purpose of the [ pairs ] section?

into account? Thank you kindly! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Scientific notation in .itp files

the value 0.35? That is, is it true that one can use e or E to specify times 10 raised to the power? Thanks for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search

[gmx-users] What is the purpose of the [ pairs ] section?

will be taken into account (at full strength), even if such pairs are not specified in [ pairs ]? I have set gen-pairs = yes, fudgeLJ = 0.5, and fudgeQQ = 0.5. Thank you for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Specifying no temperature coupling in contrast to grompp output

output refer to T-Coupling if I have set tcoupl = no? Does this make sense? (I have also _not_ specified tc_grps, tau_t, or ref_t in my .mdp file.) Thanks for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Question about dihedral angle notation

for your time! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Calculating the dipole moment vectors of functional groups

to consider), but it does not seem that g_dipoles has this. Do you think that the best way would be for me to write a bash script to call g_dipoles 1000 times with the 1000 .ndx entries? Thanks for your time! Andrew DeYoung Carnegie Mellow University -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Re: Calculating the dipole moment vectors of functional groups

will be. Thanks, Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Question about OPLS atomtypes

; I will also have solute); is it likely reasonably safe to use the above parameters for C and Cl? In other words, I would be mixing parameters from the united-atom and all-atom sections, because I have been unable to find all-atom parameters for C and Cl in CCl4. Thank you! Andrew DeYoung

[gmx-users] Type 9 dihedral in Gromacs topology

, and the multiplicity are specified. Does this mean that cp corresponds to the force constant k_phi? Thank you for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

[gmx-users] Conceptual question about the representation of dihedral angles in Gromacs

Hi, If you have time, may I ask a conceptual question about how dihedral angles are specified in force fields? Consider ethane, a two-carbon hydrocarbon (H_3C-CH_3). It has two carbon atoms and six hydrogen atoms. Call the carbons C1 and C2. Hydrogens H1, H2, and H3 are bonded to C1.

[gmx-users] A favor question: experience running Gromacs in the cloud

you for your time! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Distribution of z-coordinates for a particular index group

to computation of the number density of _each_ atom which is specified in the index file entry? Thank you for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

[gmx-users] Deuterium and the meaning of the atomic number parameter

masscharge ptype sigma epsilon HO 1 2.01580 0.418 A ; sigma, epsilon Thank you for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Turning off charges of a particular atom type

for your time. Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Re: Turning off charges of a particular atom type

Justin, Thank you for the reminder! I can't believe I forgot that important fact about ffnonbonded.itp, but I did. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

[gmx-users] Charge Group Number in itp File (cgnr)

with number 427. Will this cause inaccuracies in the simulation? I do not want to rerun all the simulations unless it seems like the missing integer will cause problems. Thanks! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Is there a way to redirect utility output to the screen, rather than to a file?

? Thank you so much for your time! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Question about cut-off values with respect to the neighbor list

groups are unlikely to move much between neighbor list updates every nstlist steps. So, my question is, am I at risk for artifacts if I use rvdw = rlist? Should I instead use rvdw = rlist? (I am using nstlist = 10 with a liquid that I anneal from 700 K down to 350 K.) Thank you kindly! Andrew

[gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond

using xpm2ps seems to say that I am correct. Thanks so much for your time. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http

[gmx-users] Re: Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond

, Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't

[gmx-users] Re: Extending a run and changing nstxout

., concatinate t=0 ns to t=10 ns and t=10 ns to t=20 ns) if needed? Andrew DeYoung Carnegie Mellon University Hi, I would like to extend a run. I ran a 10 ns simulation, and I would like to run the simulation for an additional 10 ns. Normally I would do this with the following two commands

[gmx-users] Extending a run and changing nstxout

like to reduce the frequency with which I save configurations; I would like to use nstxout = 200 instead of nstxout = 50 as in the original run. Is there any way that I can use tpbconv or a similar utility to change the value of nstxout in topol_old.tpr? Thanks! Andrew DeYoung Carnegie Mellon

[gmx-users] Re: Measuring hydrogen bonding in a specific region

if anyone has ever posted such a shell script on this list. When I look through the archives, I don't see one, but I could be wrong. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text

[gmx-users] Possible problem with g_hbond

can try differently? Thanks! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Question about the Gromacs website

below for debugging information. If this is a new install, try refreshing - the API is simply taking its time loading up! HTTP Response Status Code: 500 -- Best wishes, Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] RE: Question about the Gromacs website

Hi, I am able to access the website now. Many thanks to all for your time and effort getting it running! Andrew DeYoung Carnegie Mellon University -Original Message- From: Andrew DeYoung Sent: Sunday, July 15, 2012 2:00 PM To: gmx-users@gromacs.org Subject: Question about the Gromacs

[gmx-users] Re: Conceptual question: Why are MD production simulations usually run in the NVT ensemble?

with this reasoning? Do you think that protein folding leads to large changes in system volume, whereas in liquids the system volume is not expected to change much? Thanks so much! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Conceptual question: Why are MD production simulations usually run in the NVT ensemble?

for production MD simulations? Do you have any suggestions for helpful reading that I can do on this topic? Thank you for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text

[gmx-users] Re: Comparing amplitudes of motions in two MD simulations

Igor, I think that the utilities g_rms and g_msd may be helpful with this. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive

[gmx-users] Re: Conceptual question: Why are MD production simulations usually run in the NVT ensemble?

of the field? Are there chemists or physicists reading this that can please provide advice? Best wishes, Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please

[gmx-users] Two questions about index files

words, is there a way to make commands non-interactive _in the background_? Thank you! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive

[gmx-users] Re: Two questions about index files

that expect can be used in tandem with modification of the source code to run the Gromacs utility in the background. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed

[gmx-users] Computing vectors normal (perpendicular) to molecules

to call g_traj as many times as I have timesteps in my trajectory? Thanks so much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search

[gmx-users] What does the -don switch calculate in g_hbond?

have passed to g_hbond? Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Re: Question about documentation of -a switch in g_hbond

Justin and Mark, Thank you SO much for your help! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Bonds and atom-pairs in g_hbond

criterion _and_ the angle criterion? Probably, I have the wrong pictures of the terms hydrogen bond and atom-pair within hydrogen bonding distance in my head. Thank you for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] RE: Bonds and atom-pairs in g_hbond

is the value that I give to -r. Why are there so many more hydrogen bonds than pairs within -r, if the latter seems to be a necessary but not sufficient condition for the former? Best wishes! Andrew DeYoung Carnegie Mellon University -Original Message- From: Andrew DeYoung Sent: Monday

[gmx-users] Question about documentation of -a switch in g_hbond

between Donor and Acceptor? Which angle does -a specify? Thank you! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Selecting atom indices of residues whose centers of mass match a position range

syntax is incorrect. Can you please help me? Thank you! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Re: Calculating the average separation between two multi-atom groups

Mark, Thank you SO much for your help. I will try these suggestions. You're awesome. Andrew Hi, I have a system in a slab geometry. A surface exists at z = 0; many hydrogens protrude from the surface, and these hydrogens are mostly (but not precisely) immobile. Above the surface, there

[gmx-users] Calculating the average separation between two multi-atom groups

, then (average) H-F bond length is what I am going after, I guess. Do you know of any recipes with which to do this, or do you have any suggestions? Thanks so much! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

[gmx-users] Calculating number density using g_density

the center of mass of each molecule to represent that molecule's position. Then the center of mass of each molecule should be used to calculate the number density of molecules. Do you know if this is possible using any of the Gromacs utilities? Thank you so very much for your time! Andrew

[gmx-users] Index selection in g_potential

enter something like this: 0 3 11 The output seems to only include the potential due to the first selection (0) and seems to ignore the others. Thanks for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Question about drift in positions of frozen atoms

are not remaining frozen? Is there anything else I can try? I checked the y- and z-components other atoms, and their drifts are of the same order of magnitude. Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Should I use continuation = yes in my production dynamics following equilibration?

or no? Do you have any recommendations? Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Re: Should I use continuation = yes in my production dynamics following equilibration?

Hi Justin, Thanks so much! :-) I checked, and I am using no constraints. However, what if I were? If I did have constraints, then what would you recommend for the continuation keyword? Thanks! Andrew DeYoung Carnegie Mellon University --- If not using constraints, the continuation keyword

[gmx-users] Calculation of the components of (ionic) current using g_current

of 6144 atoms into 512 molecules which seems to imply that the code uses the topology (I provide the code with a .tpr file) to determine the connectivity of atoms. Thanks so much! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] Determining which parallelization algorithm I used

1889 802 3352011732691 804 4469311723495 750 5586511754245 235 --- Do the mentions of pd in the above .log file snippets assure me that I indeed used the -pd switch when calling mdrun? Thanks so much for your time! Andrew

[gmx-users] Re: Question about starting Gromacs 4.5.4 parallel runs using mpirun

Hi all, Thank you for your time! It seems that the code was not compiled with the --enable-mpi option. We have recompiled, and everything works now. Andrew -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Ion conductivity: current-current (auto)correlation function

you know what method it uses? Also, is it somehow possible to use g_current to calculate only the autocorrelation of the current J_z(t) along z? Thank you so very much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] -com switch in g_rdf

used the -com switch? Since the index file does not know about molecules, it wouldn't compute the center mass of each benzene molecule. But my question is, of what would it compute the center of mass? Thank you! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users

[gmx-users] Radial distribution function (RDF) in cylindrical coordinates

is perpendicular to the plates, which are parallel to the xy plane). Basically, my question is the same as that asked here: http://lists.gromacs.org/pipermail/gmx-users/2009-April/041475.html , although it doesn't seem that that post was resolved. Thank you! Andrew DeYoung Carnegie Mellon

[gmx-users] How does fourierspacing correspond to fourier_nx, fourier_ny, and fourier_nz?

, 14, 125)? Or am doing this incorrectly? Thank you so much for your time! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Re: How does fourierspacing correspond to fourier_nx, fourier_ny, and fourier_nz?

of vectors to use along +x and -x; +y and -y; and +z and -z. I think that Gromacs uses the former, but I am not sure. Best wishes, Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] Re: How does fourierspacing correspond to fourier_nx, fourier_ny, and fourier_nz?

! Andrew DeYoung Carnegie Mellon University The former for PME. The latter for plain Ewald (which you should probably not want to use). Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Units of density in the g_spatial output

units specified in the file (probably Gaussian98 does not support it). Do you have any suggestions? Thank you! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Re: What is epsilon_r?

parameter that, in fact, controls the relative permittivity of the imaginary surface. Is this true? If so, what is this parameter? Thank you for your time! Andrew DeYoung Carnegie Mellon University Andrew DeYoung wrote: Hi, What is the parameter epsilon_r mentioned in the manual (http

[gmx-users] Re: What is epsilon_r?

, then there is no dielectric at the surface (the medium surrounding the Ewald sphere)? Thank you! Andrew DeYoung Carnegie Mellon University epsilon_r should never be used with a regular force field because the balance between coulomb and other terms will be wrong. maybe we should remove the term

[gmx-users] Re: What is epsilon_r?

? Thanks! Andrew DeYoung Carnegie Mellon University No, zero means in fact infinity and this is the default. Only for very special cases should you change this. The 3dc only affects the dipole correction if I remember correctly. If you use it a refernce to a paper appears in your log file. -- gmx

[gmx-users] Inconsistent shifts in periodic molecules

is periodic/infinite). Is there anything else in particular that I can look for to try and diagnose the problem? Thank you kindly! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] ewald_rtol

sum. However, I do not see ewald_rtol specifically discussed in any of the manual sections on PME. Does this mean that ewald_rtol is only relevant for the (normal, classical) Ewald sum electrostatics? Thank you! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users

[gmx-users] What is epsilon_r?

considerably depending on the value of epsilon_r that I use in my .mdp file. Do you have any thoughts about what epsilon_r does in an all-atom descripton of a solvent? Does it provide additional charge screening? Thank you kindly! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx

[gmx-users] Classical Ewald summation

or electrostatics algorithm doesn't support parallel runs. Not starting any threads. Can you please confirm that the classical Ewald algorithm is not implemented in parallel? And that I'm imagining things thinking that classical Ewald was compatible with particle decomposition? Thank you. Andrew

[gmx-users] Pseudo 2-D Ewald Summation and Slab Geometry

ideas of what might cause this and how I can fix this? Thank you very much. Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Converting a new-version .tpr file to an old-version .tpr file

file: tpxio.c, line: 1683 Fatal error: reading tpx file (nvt2dy.tpr) version 73 with version 58 program --- This is a strange question, but is it possible to convert a .tpr file from version 73 back to version 58? Thanks so much, Andrew DeYoung

[gmx-users] Re: Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom

Greetings, Thank you so much, Mark! Do you know if it is possible to extract just the real-space part (not the reciprocal space part) of the Ewald summation? (By Ewald summation, I mean either the standard Ewald summation or PME.) Thank you very much! Andrew DeYoung Carnegie Mellon

[gmx-users] Computing the total electrostatic energy (short range, 1-4, and Ewald) of an atom

Coul-14:rest-rest 49 LJ-14:rest-rest 50 T-System --- Choices 42 and 44 are two parts of what I would like: short range Coulomb and 1-4 Coulomb energy terms for a-rest. But is it possible to somehow also calculate the Ewald term for a-rest? Thank you kindly! Andrew

[gmx-users] Calculating the electrostatic potential at a point over time

so VERY much for your time! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Do checkpoint files contain energies?

check.cpt; when I use less check.cpt, I just get nonsense characters as less attempts to read binary). Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated

be). Thank you for your time! Andrew DeYoung Carnegie Mellon University -Original Message- Andrew DeYoung wrote: Justin, Thank you so much for your help! That was really helpful. It seems that I simply append my [ nonbond_params ] section to the end of my ffnonbonded.itp file

[gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated

there is not any obvious order to use (such as N terminus, H attached to N terminus, C-alpha, etc). Thanks! Andrew DeYoung Carnegie Mellon University I haven't dissected this information for a while, but here's my understanding. Someone please correct me if I'm wrong. The list contains all

[gmx-users] Creating an atomtype where all nonbonded interactions are enumerated

don't want to just specify (single values of) sigma and epsilon. Rather, I want to enumerate all of the sigma_ij's and epsilon_ij's, using perhaps a [ nonbond_params ]-like directive. Can you please help me know how to do this? Thanks so much! Andrew DeYoung Carnegie Mellon University -- gmx

[gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated

than the bogus parameters (0 for sig and eps) for mywall in the [ atomtypes ] section? Thank you kindly! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Re: Energy exclusions for freeze groups, and the pressure

Hi, I am so sorry to bother you. If you have time, do you have any ideas or advice about my trouble below about implementing energy group exclusions to avoid spurious contribution to the pressure and virial due to frozen atoms? Thank you so very much! Andrew DeYoung Carnegie Mellon University

[gmx-users] Re: How the pressure is computed

to compute the density locally, i.e. in the part of the box actually occupied by molecules? Thank you so very much for your time! Andrew Carnegie Mellon University Andrew DeYoung wrote: Hi, I am running Gromacs 4.5.5. I am using an orthorhombic simulation box (all box angles of 90 degrees: i.e

[gmx-users] Where in the source code is the .edr file written?

quantities like density and pressure are computed and are written to the .edr file. I am not sure how straightforward this will be, but I just wanted to ask if you could point me in a general direction in the source code. Thanks so much! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing

[gmx-users] Energy exclusions for freeze groups, and the pressure

it. Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] How the pressure is computed

? Or is there a way to calculate the local pressure, just for that 54 nm^3 out of 270 nm^3? Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Literature reading on DispCorr for energy and pressure

to the Lennard-Jones potential is accomplished, and what approximations it introduces and assumptions it makes. Section 4.8 of the manual gives many details, but I am curious if you can recommend any review-type articles about this correction. Thank you very much for your time! Andrew DeYoung

[gmx-users] Calculating the center of mass of a molecule

of the center of mass of a particular molecule vary over time. g_dist computes the distance and distance vector between the center of masses of 2 groups, but I would like the centers of masses themselves, not the vector between them. Thank you kindly. Andrew DeYoung Carnegie Mellon University

[gmx-users] Resources on simulation walls

). Also, is there another name for a simulation wall? When I use Google to search for MD simulation wall, it is not clear that I am looking for the correct thing. Thanks so much for your time. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Periodic molecules and minimum bonded cut-off

Justin and Mark, Thank you so very much for your time and help. Thank you kindly. Andrew -- 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!

[gmx-users] Periodic molecules and minimum bonded cut-off

for your time! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] Advice on High Precision Structure File Formats

detailed information about the .g96 file format. Unfortunately, my institution I do not think has a GROMOS-96 license, so I cannot access its manual. Between .pdb and .g96, which would you recommend? Or is there any other structure file format that I am not thinking of? Thanks so much. Andrew

[gmx-users] Pressure coupling and membrane-type simulations

that would help me understand and choose between the pressure coupling types? Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] xy option in g_rdf

me visualize what the -xy option does? Thanks so much for your time! Andrew DeYoung Carnegie Mellon University -- 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

[gmx-users] g_x2top

colleague's simulation, when bonds were stretched and compressed, etc. Do you have any advice whereby I could still use this non-starting configuration? Thanks so much. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Re: Recommended parameters for NVE simulation of SPCE water

Dear Professor Shirts, Thank you so much. I really appreciate your time in responding to my post and providing advice. I will try your suggested parameters for reasonably good energy conservation, and I will let you know how it goes. Thanks again for your time. I will be in touch. Andrew

[gmx-users] Re: Improving Energy Conservation in NVE Simulation of Water

-rescale was poor; in my next simulation perhaps I should try Nose-Hoover) and possibly intergration algorithm, rather than related to cutoff lengths. Do you think that this is a correct interpretation? Thank you very much. Andrew DeYoung Carnegie Mellon University Andrew DeYoung wrote: Hi

[gmx-users] Re: Improving Energy Conservation in NVE Simulation of Water

with tau_t = 2 ps. What kind of temperature coupling do you typically use or recommend? Thanks, Andrew Andrew DeYoung wrote: Hi, I have been simulating 1000 SPC/E water molecules in the NVE ensemble (by using tcoupl = no and pcoupl = no). In these simulations, I am considering only Lennard

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