[gmx-users] version 3.3.1 .tpr file with version 3.2 g_order

to run the version 3.3.1 .tpr file through the version 3.2 tpbconv program to get a new .tpr file, or would it yield the same error? Thanks for any suggestions --Michael Skaug University of California Davis ___ gmx-users mailing listgmx-users

Re: [gmx-users] free energy

One other thing I would point out is that the solvation free energy is dependent on concentration. you will get a different result with 4 polymer chains vs 3 vs 3, etc. Make sure you understand the dependence. Also, the free energy will depend on the polymer chain length. Polymer and finite con

[gmx-users] PMF from pull code, unexpected results

no additional constraints but with "comm_mode = Angular" i get results somewhere inbetween the two cases above. my specs: Gromacs version: 4.5.3 Linux 2.6.35-23-generic Ubuntu x86_64 gcc version 4.4.5 I am not sure whether i overlooked something in my input, or whether there's

[gmx-users] Re: PMF from pull code, unexpected results

, as in: "removing" something thats negative) is that correct? ... and if so, why does it, seemingly, not apply in the above Gedankenexperiment? Yours truly (and maybe some other people) would really appreciate if somebody in the know would clarify that! thanks in advance! Michael

[gmx-users] PMF from pull code, unexpected results

> Michael: your mdp options indicated using US and my stance is that, > using >US, you are incorrect to say that "And you will get the SAME > result if you >do this calculation in one or in three dimensions > (pulldim NNY or pulldim >YYY)". this has nothin

[gmx-users] topology files for ligands in MD Simulation under OPLS AA force field

mircial at sjtu.edu.cn mircial at sjtu.edu.cn wrote > I am using GROMACS package to do molecular dynamics > simulations under OPLS_AA force field. I encounter > some problems when preparing the topology files > of small molecules (ligands).My questions are as follows: > 1, how to chose the atom

Re: [gmx-users] Possible free energy bug?

Hi, all- Have you tried running constraints = hbonds? That might eliminate some of the constraint issues. Much less likely for LINCS to break or have DD issues if only the hbonds are constrained. 2 fs is not that big a deal for the heteroatom bonds. Best, Michael On Thu, Mar 10, 2011 at 8

Re: [gmx-users] autocorrelation time of dVpot/dlambda?

> I am doing free energy calculation in Gromacs and want to get an error > estimate of my results. Is it possible to compute the autocorrelation time > of dVpot/dlambda in Gromacs using a certain length of trajectory such as 10 > ns? Thanks a lot The amount of simulation time required to compute t

[gmx-users] thermostats, canonical distribution, and stochastic dynamics

er: i) is there any limit to the size of tau_t I am supposed to use? or ii) is there any other way to accelerate convergence? FTR: I also tried using two tc_grps (one for each particle) but, at least qualitatively, i see the same results. thanks in advance for any help! regards, Michael ===

[gmx-users] IMPLICIT SOLVENT IN AMBER

I recently came across a paper (J. Phys. Chem. B 2005, 109, 10441-10448) in which the authors found that using implicit solvent with explicit ions you easily end up with all the ions cuddling up in clusters ... which is obviously an artefact. That is, if you do use this combination you certainl

[gmx-users] pull forces

are oscillating as expected, but the forces on the reference group are close to, but not exactly(!) zero. i am not sure how to interpret this ... cheers Michael -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] mdrun

e searched the net for this error and didn't find any answer. Did anybody see this error? and what should i do with it.. Thanks, Michael -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromac

[gmx-users] Re: Is there still interest in rigid-body simulation?

Ignacio, I would be very interested in a rigid body capability. On 3/28/2011 5:45 AM, gmx-users-requ...@gromacs.org wrote: Is there still interest in rigid-body simulation? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] speed issue, gmx runtime estimate = f(t)

x27;d appreciate any suggestions! (below is my mdp file.) cheers, Michael mdp file: integrator = md ; dt = 0.001 tinit= 0 nsteps = 10 nstxtcout= 0 nstxout = 1000 nstvout = 0 nstfout

[gmx-users] PME

Elisabeth, You CAN, in fact calculate the contribution of the reciprocal part of the PME energy to the binding energy between two components in a heterogeneous system, its just quite tedious... say, your system is molecules A and B for which you want to know the interaction energy, and the rest

[gmx-users] PME

Elisabeth wrote: > The point is in my case there is no option other than ignoring LR since LR > is not covered by shift or switch functions but at least what PME reports > for SR is more accurate. not really ... PME electrostatic energy is a sum of two contributions LR and SR ... and only the SU

[gmx-users] sugar force fields

which making sugar topologies is as straight forward as making topologies for amino acids, or if there is no such thing for which FF is making a sugar topology the least tedious? BTW: I want to model simple sugar molecules, monomers, dimers (no polymers) thanks! Michael -- gmx-users mailing

[gmx-users] unexpected results with stochastic dynamics

seen something similar ? i'd appreciate any suggestions! thanks Michael -- 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&

Re: [gmx-users] implicit solvent LINCS errors

ling= no constraints = hbonds constraint_algorithm = lincs morse= no --- On 5/30/11 8:45 PM, Michael D. Daily wrote: Thanks for the recommendations everyone. I tried all of the mdp changes recommended by Justin (increase rlist, rvdw, etc to 2.0; change T-coup

Re: [gmx-users] oplsaa vs. charmm

https://sites.google.com/site/thomasevangelidishomepage/ -- Michael D. Daily, Ph.D. Postdoctoral Fellow Qiang Cui group Department of Chemistry University of Wisconsin-Madison -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/

[gmx-users] AFM Simulation

Hi everyone. I'm doing a simulation of a system where a peptide is linked to a surface and an AFM tip is brought in contact to do force measurements. The AFM tip moves very slowly (1nm/ms), so I'm simulating stationary tips at various distances. Does anyone know the most direct measurement f

Re: [gmx-users] Programs to add residues

> > I've also seen people use PyMOL's builder to do this. Either way, you'll need to take (a lot of) extra care to minimize your linker and make sure that it looks reasonable. -Michael > Nevertheless, I'd suggest simply omitting that part of the protein and > capp

Re: [gmx-users] Exchange interval in REMD

> It also depends whether or not you use constant pressure, in which case it > makes sense to increase the time to long enough to let the volume relax. > I still do not understand why people do NVT REMD, because it makes all but > one replica have a pressure that is not the ambient pressure. If al

Re: [gmx-users] BUG: Free energy calculation

system so problems are documented. I'm also working on the updates to free energy code in 4.6, so I want to make sure this will be solved there as well. Best, Michael On Fri, Mar 23, 2012 at 7:16 AM, Sabine Reisser wrote: > Hi Mark, > > with FE, without PR : same error > without FE

Re: [gmx-users] BUG: Free energy calculation

Sabine, thanks for filing it in redmine! Having a record helps a lot. Can you also attach all your input files to the redmine filing? It can only really be debugged if the input files you used are included. Best, Michael On Fri, Mar 23, 2012 at 9:11 AM, Justin A. Lemkul wrote: > > &g

Re: [gmx-users] poor performance in Hemiltonian Replica Exchange

unless I can reproduce the error you are describing out of the box, its unlikely I will be able to find it. Additionally, it would be easiest if the files were deposited as a redmine bug report, so that the information is centrally located. Best, Michael On Thu, May 10, 2012 at 12:23 PM, francesco

Re: [gmx-users] REMD question

Gromacs already supports replica exchange -- what particularly are you implementing? Equilibration of pressure is always a good idea -- even if you are running NVT simulations, you want to get them to be at the equilibrium volume for your system and temperature choice, which will require equilibra

Re: [gmx-users] Configurational bias Monte Carlo

There's a fair amount of interest for more general support for Monte Carlo methods in GROMACS 5.0. However, there is no any current support for configuration bias Monte Carlo (or any other kind of MC) currently in the code. On Fri, Jun 1, 2012 at 12:10 PM, Benjamin Haley wrote: > Hello, > >   I

Re: [gmx-users] Re: Re: Is vacuum simulation NVT?

> Could you tell me is there any difference of different Tau_t ussage ( > inverse friction in case of Stochastic dynamics) for simulation of > water-soluble as well as membrane-proteins ? In the first case I'm > using tau_t 2ps that is lower than internal water friction. In the > second case one pa

Re: [gmx-users] meta-dynamics in gromacs-4.6

I assume PLUMED will be implemented for Gromacs 4.6, as many PLUMED developers use Gromacs. Perhaps any PLUMED lurkers on the list can speak up. . . . On Wed, Jan 16, 2013 at 9:20 AM, Mark Abraham wrote: > The GROMACS team has no plans for that. The usual problem here is that > everybody would l

Re: [gmx-users] Expanded Ensemble and Gromacs 4.6

Hi, Joakim- Expanded ensemble is still a bit experimental. I don't immediately see any problem that jump right out, but if you go to http://redmine.gromacs.org/ and file a bug report, including giving example files that cause the problem, I can take a look at it. On Tue, Feb 5, 2013 at 6:00 AM,

Re: [gmx-users] The time for the temperature and pressure coupling

The coordinates and velocities that are printed (and that are used to calculate the properties like energy, virial, etc) are always consistent with the constraints. The exact order of how things are done often depends on the integrator. For example, velocity scaling can be done before or after co

Re: [gmx-users] The time for the temperature and pressure coupling

Ah, now perhaps I see that I misread the question - it could have been phrased more clearly. If Erik understood it correctly, then the answer to the question is: It depends on the integrator. The simulation is not constrained to a particular temperature or pressure - rather, the dynamics are modi

Re: [gmx-users] g_bar for larger systems (protein-protein interaction)

My personal opinion is that for large protein-protein calculations, the free energy should be computed through potential of mean force calculations, NOT alchemical methods, using the endpoints (properly corrected) to determine the free energy of association. There are a number of tutorials and exa

Re: [gmx-users] CMAP and Free Energy

There is no theoretical reason to exclude it. The CMAP code is routed differently in the logic, and was put in at the same time the free energy code was, so it's just software engineering issues. This is a good candidate for inclusion in 5.0 if enough people request. On Wed, Feb 27, 2013 at 1:04

Re: [gmx-users] Hamiltonian replica exchange umbrella sampling with gmx 4.6

Hi, Joakim- Hamiltonian exchange only should work if there is a lambda coupling parameter that defines the potential at each state. You need to define your pulling potential so that the coupling-lambda parameter can be used to define the different pulling location centers along your trajectory.

Re: [gmx-users] Re: Hamiltonian replica exchange umbrella sampling with gmx 4.6

Great -- if it doesn't seem to be working the way it should after some playing around, then submit it as a redmine issue, and I'll take a look. On Fri, Mar 8, 2013 at 2:51 AM, Joakim Jämbeck wrote: > Dear Michael, > > Thank you for your reply. > > Yes, it is relative

Re: [gmx-users] Re: Hamiltonian replica exchange umbrella sampling with gmx 4.6

more general multistate lambda vector formalism for 5.0. If you have suggestions, let me know. I'd be happy to look over input files or give additional advice on a specific setup. On Tue, Apr 2, 2013 at 12:52 PM, Dejun Lin wrote: > Hi Michael, > > Do the codes now support walk

Re: [gmx-users] Free Energy Calculations in Gromacs

You have to change atom types. For example: [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon h1h1 0. 0. A 2.47135e-01 6.56888e-02 h1_pert h1 0. 0. A 2.47135e-01 3.56888e-02 ; perturbed The

Re: [gmx-users] issue in replica exchange

Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham wrote: > On Thu, May 2

Re: [gmx-users] issue in replica exchange

l try gmx-4.6.1 > > On May 2, 2013, at 2:26 PM, Michael Shirts wrote: > >> Quick check here -- is 4.6 behaving correctly? I actually spent some >> time working on REMD in 4.6, and it seems to be behaving correctly in >> my hands with temperature and pressure cont

Re: [gmx-users] issue in replica exchange

I > turned it off during compilation … > > You could try to run on particle decomposition to see if you get a problem … > it should one quite quick. > > On May 2, 2013, at 2:36 PM, Michael Shirts wrote: > >> Both. So if 4.6.1 doesn't work, I want to know so we

Re: [gmx-users] issue in replica exchange

Summarizing! On Fri, May 3, 2013 at 12:31 AM, XAvier Periole wrote: > > Are confirming that you reproduce the problem with gmx-4.6.1 or simply > summarizing in case we lose track :)) > > On May 2, 2013, at 23:31, Michael Shirts wrote: > >> So to summarize -- the pr

Re: [gmx-users] Re: Nose-Hover chains for membrane protein simulation

I can't think of any instance where nose-hoover chains provides an advantage over nose-hoover in a large system -- all the demonstrations of superiority are in model systems that are not particularly chaotic. As the system gets more chaotic, it matters less. I would go with md, nose-hoover (w/o c

Re: [gmx-users] Re: Nose-Hover chains for membrane protein simulation

that are solved by NH chains are for small toy systems. On Sun, Jun 2, 2013 at 2:17 AM, James Starlight wrote: > Michael, > > > thanks for suggestions. > > the main reason of ussage N-H with chains is the assumption that simple N-H > does not provide ergodicity of the system

Re: [gmx-users] What does --enable-fahcore mean?

It only matters for running on Folding@Home. For other users of gromacs, it doesn't do anything. On Tue, Jun 26, 2012 at 3:50 PM, Bao Kai wrote: > Hi, all, > > I am wondering what the --enable-fahcore option of configure means.  I > got the explanation from configure --help of "create a library

[gmx-users] tabulated potentials and soft core free energy - this should not work ....

s for any advice! michael mdp: integrator   = sd nsteps   = 10 dt   = 0.002 ; pbc  = xyz nstcomm  = 100 comm_grps    = System ; nstxtcout    = 0 nstenergy    = 100 ns

[gmx-users] g_bar ... the right answer for the wrong reason?

Hi, i just performed a free energy TI calculation, to get the free energy of solvation of water in water (the chemical potential of water) i stuck closely to the templates given in the tutoral by justin lemkul. The final result i get with g_bar looks good, and the number is within the error-bars

[gmx-users] problem with git/4.6

hi as suggested in: http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6 i do: prompt> git clone git://git.gromacs.org/gromacs.git Cloning into 'gromacs'... remote: Counting objects: 119131, done. remote: Compressing objects: 100% (21428/21428), done. remote: Total 119131 (delta 100642), re

Re: [gmx-users] problem with git/4.6

id here ? if this is so it might be a good idea making g_bar read tpr files to give a warning in such a case ... i guess for now i'll wait for a stable 4.6 - any ideas when this will be there? thanks! michael -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mail

[gmx-users] BAR gives different result than TI

eparate calculations (mutation in vacuum and mutation in solvent) compare? cheers michael === Why be happy when you could be normal? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allo

[gmx-users] water with atom-based cut-off ...

t now constraints are not applied to waters at all (O and H look as if they move independently) it also didn't help renaming the water molecule, residue and atom names ... any suggestions on how i can apply atom-based cut-off with lincs or shake to water? thanks

[gmx-users] tricky business

her in terms of methods nor references) I don't know what P. H. Hünenberger said in his talk, but i am mostly concerned about correction terms discussed here: J. Phys. Chem. 1996, 100, 1206-1215 thanks, michael === Why be happy when you could be normal? -- g

Re: [gmx-users] BAR gives different result than TI

The implementation of BAR in gromacs is pretty hard for me to follow because of how everything is stored noncompactly in the histogram. In 4.6, both can be computed from the same dhdl.xvg file, so it might be easier to track down possible bugs. On Fri, Jun 29, 2012 at 2:24 PM, David van der Spoel

Re: [gmx-users] lincs with mttk

ncy than the nonbondeds, which will be another useful way to get longer times steps. We also have planned to implement a Monte Carlo barostat, which will give exactly the correct NPT distribution for any integrator. Best, Michael On Fri, Jul 27, 2012 at 2:01 PM, Katie Maerzke wrote: > Hi all - &

[gmx-users] NMA and g_nmeig segmentation fault

Hello All -- I'm trying to do a normal modes analysis of a fairly large crystal system (~20,000 atoms) in double-precision GROMACS. The system is xy periodic with 2 9-3 walls, and has periodic molecules. I first minimized the structure with L-BFGS to 1e-5 tolerance with switched vdW interactions an

Re: [gmx-users] When to use Dispersion Correction for Lipid Bilayers

n, it will be possible to parameterize lipids that behave correctly. Best, Michael On Sun, Aug 19, 2012 at 3:16 PM, David Ackerman wrote: > Hello, > > I was wondering when it is appropriate to use Dispersion Correction > for lipid bilayers, or which setting (no, EnerPres, or Ener) is

Re: [gmx-users] BAR / g_bar problems

(?), but we can plan now. Note that withe errors this big, 100-200 ps should be enough to see what's going on, so it can be done rapidly. Drop me a line off the list to figure out details? Best, Michael On Fri, Aug 24, 2012 at 9:22 AM, David van der Spoel wrote: > Hi, > > we have terrib

Re: [gmx-users] Re: v-rescale

I've done some extensive testing (paper on testing method in the works) and vrescale gives a very accurate ensemble very well for NVT. Parrinello-Rahman and MTTK are the only algorithms that are correct for NPT. Berendsen barostat is not. Note that there is a bug with vrescale + md-vv + that is f

[gmx-users] Experiences with Gromacs scaling on US supercomputer centers?

up tweaks, but let's start with 4.5 scaling info! Best, Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/

Re: [gmx-users] Re: Fast exchanges for REMD

> However, the time value (4 in this example) is limited to 6 digits. Sounds like this should be increased? There's a pending change to replica exchange, so this could be added to 4.6 without disrupting the release timing. On Wed, Sep 26, 2012 at 11:22 AM, Andreas Zink wrote: > Dear all, > > I

Re: [gmx-users] pressure_coupling

Hi, all- There are some issues with MTTK + constraints that are being worked out for 4.6. The good thing is, I have developed some sensitive tests of the correct volume distribution (see http://arxiv.org/abs/1208.0910) and the errors in PR are very, very small. I would recommend using md + PR for

Re: [gmx-users] Re: pressure_coupling

It's in review with JCTC right now. On Thu, Nov 22, 2012 at 2:19 PM, ABEL Stephane 175950 wrote: > Hello, > > This is a very nice and interesting work, Michael. Thank you for the efforts > you made in writing this paper. I hope you will publish it. >

Re: [gmx-users] Question about conserved energy in MTTK

Hi, all- I would recommend using Parrinellio-Rahman + Nose-Hoover md + at least until 4.6. A random-walk drift in the conserved energy is actually what MTTK gives -- it's not as conserved as, say, energy conservation, it just has an expectation value of zero drift over time, which means that the

Re: [gmx-users] Is vacuum simulation NVT?

> In the absence of PBC, you simply have an infinite system. In a loose > sense, that may be NVT, but V is infinite, so whether or not you can > consider that to be constant or not is theoretical math above what I know :) A real molecule in vacuum is usually NVE -- it is not coupled to the enviro

[gmx-users] Charge groups in Charmm for lipids

Hi, I'm making a lipid topology for DPPG in the charmm forcefield in gromacs 4.5.  I'm putting it together from pieces of what already exists as suggested in the charmm files.  I noticed that there are charge groups in the original charmm files, and these were reflected in the gromacs topology i

Re: [gmx-users] Charge groups in Charmm for lipids

that should help in making a CHARMM27 DPPG rtp entry (if you wish to use the CHARMM27 lipids rather than the CHARMM36 ones). Cheers Tom On 06/08/11 00:22, Michael McGovern wrote: Hi, I'm making a lipid topology for DPPG in the charmm forcefield in gromacs 4.5.  I'm putting i

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

= 1.1 This should work quite well -- you might get some drift after 1-2 ns, but not much. I'm working on developing suggested PME parameters right now for highly quantitative work, but it's not quite ready yet. Michael Shirts Assistant Professor De

Re: [gmx-users] Hamiltonian replica exchange?

Hamiltonian replica exchange is planned for 4.6, and is being beta tested by some users. On Tue, Aug 16, 2011 at 2:39 PM, Sanku M wrote: > Hi, >    I was wondering whether hamiltonian replica exchange simulation has been > implemented in latest version of  gromacs . Or, is there any other way of

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

veloping suggested PME parameters > right now for highly quantitative work, but it's not quite ready yet. > > > > Michael Shirts > Assistant Professor > Department of Chemical Engineering > University of Virginia > michael.shi...@virginia.edu > (

[gmx-users] Using genbox to REMOVE solvent

Hi all, I am looking for a relatively easy way to make minor modifications to a solvated system in gromacs without having to replace the whole solvent layer. Specifically, I'm swapping out some molecules (technically, just swapping residue and atom names) in a MARTINI model and I think this cause

Re: [gmx-users] Using genbox to REMOVE solvent

rrible starting structure - fortunately the system can be regenerated from scratch with a new lipid config overnight. On Wed, Aug 17, 2011 at 11:54 PM, Mark Abraham wrote: > On 18/08/2011 4:32 PM, Michael Daily wrote: > >> Hi all, >> >> I am looking for a relatively easy way to ma

Re: [gmx-users] Using genbox to REMOVE solvent

And I am happy to report that this method produces a viable starting structure :) On Thu, Aug 18, 2011 at 7:02 PM, Michael Daily wrote: > I tried an experiment similar to yours - after converting the POPE's to > POPC's when I remove all waters that are near the (lipid-emulsified

[gmx-users] surface area calculations for MARTINI

ws 2.35 A as the vdw radius for all lipid groups, which I fear will cause inaccurate calculations in APBS. Has anyone had this problem before? Mike -- ==== Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (form

[gmx-users] MARTINI / all-atom mapping

;, 'O11','C12'], 'GL1' : ['C13', 'O14', 'C15', 'O16'], 'GL2' : ['C32', 'O33', 'C34', 'O35'], etc. For some atoms it's obvious which MARTINI groups they belong in, but o

Re: [gmx-users] MARTINI / all-atom mapping

ted. Mike On Tue, Aug 30, 2011 at 3:06 AM, XAvier Periole wrote: > > it must be some example of mapping lipids on the website: cgmartini.nl > > On Aug 30, 2011, at 3:55 AM, Michael Daily wrote: > > Hi all, > > I am trying to reverse-map some martini lipids to united a

[gmx-users] Questions regarding REMD simulation

such as the demux.pl script?) Thanks, Michael -- 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 t

Re: [gmx-users] Membrane protein simulation

it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison) -- gmx-u

[gmx-users] opls parameters fir gramicidin terminal groups

hanks, -- Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users P

[gmx-users] TI/FEP, BAR, and topologies

of worms) thanks in advance for any help! cheers Michael -- 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

Re: [gmx-users] Question about Justin's Free Energy Tutorial

by changing the top files. Best, Michael On Thu, Oct 6, 2011 at 2:42 PM, Justin A. Lemkul wrote: > > > Fabian Casteblanco wrote: >> >> Hello Justin, >> >> I have a question about your tutorial.  If I want to mutate one small >> group of a molecule, I would

Re: [gmx-users] FEP

FEP is a poorly defined term. It can either mean 1) making small changes 'alchemical' changes in the molecules and computing the free energies by any method (BAR, TI, etc), or 2) it can mean specifically computing the free energies by exponentially averaging the potential energy differences. Basi

Re: [gmx-users] FEP

> So BAR is only > referring to the mathematical code used to calculate the overall free > energy for the FEP, correct? Yes. The information required is the same, with the exception that exponential averaging requires energy differences from only one state, whereas BAR requires energy differences

Re: [gmx-users] How DispCorr influsnces pressure

e: http://pubs.acs.org/doi/abs/10.1021/jp0735987 for some additional information. Members of the Gromacs team are working behind the scenes for various possible solutions to the problem for nonisotropic systems. Don't expect anything until 5.0, though. Best, Michael -- gmx-users mailing lis

Re: [gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

> Is anyone aware of any benchmark analysis about the implementation of the > amber99sb force field (or any of its variants: 99sb-ildn, 99sb-nmr) in > GROMACS and AMBER. I am interested to know in what extend the energies > correlate and if the results agree with experimental data. Whether the res

[gmx-users] Charmm Sugars/carbohydrates

Hi everyone. I'm doing a simulation in gromacs using the charmm36 parameters from the gromacs website. The parameters don't seem to have carbohydrates, which are part of the charmm36 force field. In particular, I need parameters for trehalose. Is there anywhere I can find these parameters in a

[gmx-users] shell molecular dynamics

ACS manual, online tutorials etc. Can anybody help me with this problem or guide me to appropriate tutorial. Thanks in advance. Michael -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.o

Re: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field

> It should also be noted (and obvious now that I actually look into it) that > using dispersion correction results in both the latent heat of vapourisation > and density of the alkanes being over estimated (for both Cut-off and > Reaction Field, and by the same amount). That may not be quite t

Re: [gmx-users] Re: Free Energy Calculations in Gromacs

An important final point is that you can always see EXACTLY what grompp is putting into the B state by running gmxdump on the resulting tpr. It's a LOT of information, but all in text all the interactions are listed explicitly there. On Mon, Jun 10, 2013 at 6:20 PM, Justin Lemkul wrote: > > > On

Re: [gmx-users] Re: Enthalpy Confusion

If you are computing enthaply in the NPT ensemble, P is constant, and is the applied pressure. The "pressure" quantity calculated from the KE and the virial is not the pressure. It is a quantity that when averaged over time is equal the pressure. Only the average is meaningful macroscopically.

[gmx-users] 2013 GROMACS USA Workshop and Conference

and Conference Steering Committee Michael Shirts (chair) Angel Garcia Berk Hess Yu-Shan Lin Erik Lindahl Peter Kasson -- 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

Re: [gmx-users] Re: Enthalpy Confusion

> or should i be doing < U+*ref_p > = ? More specifically, + *ref_p = H isn't really meaningful thing. I mean, you can define something such that = H, but that's not really thermodynamics. > example system gives = -1168 kJ/mol and i find = -725 kJ/mol either Interesting. What material at

Re: [gmx-users] Re: 1-4 interactions free energy calculations

Hi, Sonia- Gromacs 4.6.2 (some bug fixes vs 4.6.1) with the example files you point out from Alchemistry.org should work well for expanded ensemble. David Mobley and I have been validating expanded ensemble and replica exchange, and the files posted there now are stable for all sizes of systems,

Re: [gmx-users] a question concerning on entropy

No. This is a statistical mechanical issue, not a GROMACS issue. For interacting systems, entropy is a quantity describing the system as a whole, and cannot be defined for different parts of the system, at least not in any way such that the individual components can be added together. I'm also n

Re: [gmx-users] Larger number of decimal places for coordinates with velocities

Have you checked out the -ndec option for trjconv? If you have a high precision format (.trr, or .xtc if they are stored with sufficient precision) you can print out a .gro file (that gromacs can read) with higher precision. Gromacs can read .gro files with increased precisions in the coordinates

Re: [gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

Hi, all- This not a problem with W-L, but is instead something that is wrong with a particular combination of mdp options that are not working for expanded ensemble simulations. W-L can equilibrate to incorrect distributions because it decreases the weights too fast (more on that later), but that

Re: [gmx-users] window exchange umbrella sampling

You need to have different pull parameters at the end states. Right now, pull-kB1 is not defined in your code, so there is nothing to interpolate to: it assume pull-kB1 = pull-k1. Longer scale -- one would want to define reference distances that change with lambda within the same simulation, but l

Re: [gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

- I'd have to dig a bit to get you good results on that . . . On Tue, Jul 16, 2013 at 3:19 PM, Dejun Lin wrote: > Hi Michael, > > Thanks for the reply. Just a quick follow-up. Do you think the overlap of > energy histogram between different lambdas matter for lambda-dynamics in &g

Re: [gmx-users] Re: window exchange umbrella sampling

Ah, this is a force field issue -- urey-bradley terms are not supported free energy calculations. However, since only restraints are changing, this warning doesn't really need to be there. It would be relatively simple to put in a check to allow this to work, but it might take a week or two to get

Re: [gmx-users] Re: window exchange umbrella sampling

4.5.7 does not support Hamiltonian exchange. It says all properties are the same, because all the temperatures and pressures are the same -- it won't switch the umbrellas. On Wed, Jul 17, 2013 at 3:30 PM, Parisa wrote: > Hi Michael, > > I think that this is an issue with the gro

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