Re: [gmx-users] FEP and loss of performance

/  still I think that there must be some underlying coding issue >> > (probably />>/  one that only exists because of a reasonable assumption >> > that nobody />>/  would annihilate the largest part of their system). >> > />>/ >> > />>/  Ch

Re: [gmx-users] FEP charged molecule cuestion

sts/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 > -- David Mobley dmob...@gmail.com 504-383-3662 -- gmx

[gmx-users] dihedral restraints documentation

ld be documented in the manual since (with this behavior) knowing what value of dihre-fc one is using is critical to knowing what dihedral restraint strength one is using. Thanks. -- David Mobley dmob...@gmail.com 504-383-3662 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromac

Re: [gmx-users] Regarding free energy calculation

Hunenberger papers from J. Chem. Phys (2006 or 2007) and references therein. The good news is that for simple spherical ions K&H have worked out the relevant corrections. The bad news is that if you move away from simple spherical ions you've got problems. David Mobley On Fri, Dec 16, 2011 a

[gmx-users] where are GB parameters stored?

d like to be able to look at the table of existing parameters). I've been looking through the "top" directory and can't find them anywhere. Can anyone give me a pointer to where they are? Or are they hardwired into the code somewhere? Thanks so much, David -- David Mobley dmob

[gmx-users] Fwd: fixed "3.3.3"?

y components (which is yet another reason why we need a patched 3.3.x to compare to), given the number of times we were burned by free energy bugs in 3.3.x. Thanks for your help. David Mobley, Ph.D. Assistant Professor of Chemistry University of New Orleans New Orleans, LA 70148 dlm

[gmx-users] Re: Free Energy Calculation

Hi, Sorry for the delay answering. These questions are better put on the GROMACS users list. 1) Yes -- the Berendsen barostat does not sample the correct distribution of pressures. 2) Regenerating velocities is fine for a couple of reasons: (a) we are after thermodynamics, not dynamics, a

Re: [gmx-users] Re: Free Energy Calculation

-Original Message- > From: gmx-users-boun...@gromacs.org on behalf of David Mobley > Sent: Thu 8/6/2009 2:38 PM > To: Mauricio Carrillo Tripp > Cc: Discussion list for GROMACS users > Subject: [gmx-users] Re: Free Energy Calculation > > Hi, > > Sorry for the delay answering

Re: [gmx-users] Re: Free Energy Calculation

hen what guarantees that the the volume/density is correct > at the end of the equilibration phase when the user is advised to switch to > NVT? > > Peter Nagy > The University of Toledo > > -Original Message- > From: gmx-users-boun...@gromacs.org on behalf of David

Re: [gmx-users] FEP problem with lambda perturbation 1 to 0.95

I agree with Carsten. See perhaps the discussion at www.alchemistry.org as well. On Fri, Aug 7, 2009 at 2:35 AM, Carsten Kutzner wrote: > On Aug 6, 2009, at 10:57 PM, Ragnarok sdf wrote: > > I am performing FEP do obtain the dimerization of a protein in >> membrane. The lambda intervals i am us

[gmx-users] Fwd: md.c for 3.3.3

Erik On Jul 29, 2009, at 12:18 AM, David Mobley wrote: > Erik, > > Here's the fixed md.c for 3.3.3. It is a one-line fix and is > commented with DLM. > > Please note that the basic fix was developed by you guys in this > Bugzilla: http://bugzilla.gromacs.org/show_bug.cgi?

[gmx-users] Re: script to constraint distance between ligand and protein

nd and > protein, I have individual .top and .gro files for protein and ligand. > > Thanks in Advance > -- > Best Regards > SUNITA GUPTA > David Mobley dmob...@gmail.com 504-383-3662 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] off topic: graduate school opportunity

ile I do not currently have RA support for students, I anticipate having some in the near future, and in the meantime anyone joining my group would be supported by a TA position. Thanks for your time. David Mobley, Ph.D. Assistant Professor of Chemistry University of New Orleans New Orleans, LA

Re: [gmx-users] charge changes in free energy calculations

Hi, As long as you end up with the same charge in the initial and final states, you should be OK. It's only if your total transformation involves a change of net charge that you need to worry. So you should be fine if you turn off the charges on D, change the LJ interactions, and turn back on the

Re: [gmx-users] Free energy of transfer with accuracy

w exactly you're doing the transformation and could use more detail on how you've set this up. A more straightforward (and easier?) way to do this would be to transfer the solute to vacuum from each solvent and then take the difference in the vacuum transfer free energies. Please clarify w

Re: [gmx-users] Relative Binding Free Energy Calculation

Bob, > When performing a relative binding free energy calculation, I > understand that it is a good practice to separate the transformation > of charges of the ligand and the transformation of vdW parameters into > two calculations. However, is it advisable to completely discharge the > ligand bef

Re: [gmx-users] Free energy of transfer with accuracy

- Bloco B, Sala 1048 > 09210-170 Santo André - SP Brasil > +55.11.4437-8408 > skype: eefileti > http://cromo.ufabc.edu.br/~fileti/ >> >> >> -- >> >> Message: 4 >> Date: Thu, 11 Dec 2008 07:24:26 -0600 >> From: "David Mobley&q

Re: [gmx-users] Free energy of transfer with accuracy

my data suggests this is likely. :) Personal experience tells me that this would probably be the case but I haven't ever seen a publication on this. David David Mobley, Ph.D. Assistant Professor of Chemistry University of New Orleans New Orleans, LA 70148 dlmob...@uno.edu Office 504-280-6445 Fax

Re: [gmx-users] Free energy of transfer with accuracy

ver soft core functional form you use. This just means >> you will need to run longer simulations in this regime. >> >> Anyway, long story short, I suggest two things: (a) Make sure you turn >> off partial charges on C60 (without using soft core) before turning >> off the LJ

Re: [gmx-users] Large dV/dlambda value at lambda = 0

Bob, > I'm computing the relative binding free energies of DNA bases on a > nanotube using the protocol listed here: > http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial > I'm using the following steps: > 1. Turn off all charges on base > 2. Transform LJ parameters > 3. Turn o

[gmx-users] rcoulomb, rlist

y be some sort of an underlying problem here. On my list of things to do is to see whether I still get the same results in GROMACS 4. Thanks for your help, David Mobley ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listi

[gmx-users] Re: free energy with TIP4P bug fixed

mized loops, for sure it was in 3.3. I have fixed this for the upcoming Gromacs 4.0.4 release. I assume this bug also caused the cut-off dependence that David Mobley observed. I have done a lot of free energy calculation with tip4p and never noticed any problems. This was because I alway

[gmx-users] TIP4P/TIP4P-Ew bug potentially affecting all calculations done with TIP4P with some (few?) exceptions

ultimately have to submit errata for two different papers I've published in which I used the TIP4P-Ew water model in combination with GROMACS. I urge you to check your own studies that have used TIP4P/TIP4P-Ew and see if they are affected. David Mobley Assistant Professor Department o

Re: [gmx-users] free energy with TIP4P bug fixed

doing some testing, but I anticipate that I will ultimately > have to submit errata for two different papers I've published in which > I used the TIP4P-Ew water model in combination with GROMACS. I urge > you to check your own studies that have used TIP4P/TIP4P-Ew and see if > they

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Perhaps this is obvious, but typically you only want to do free energy perturbation if you are interested in computing a free energy difference. If you are merely interested in structural properties of a different system (in this case, the protein without the copper there) you can simply make the c

[gmx-users] shake for water

All, A quick question on constraints... I'm using TIP4P-Ew in gromacs 3.3.2 and am concerned with reproducing energies from another code very precisely for several specific snapshots. I am doing a zero-step mdrun of a setup with one small molecule and two tip4p-ew water molecules. Anyway, I have

Re: [gmx-users] shake for water

Berk, > Another question, just to be sure. > Have you actually checked that the other code really gets the distances > right up to 1e-12? Yes. > Berk > >> Date: Thu, 5 Feb 2009 12:03:21 -0600 >> From: dmob...@gmail.com >> To: gmx-users@gromacs.org >> Subject: [gmx-users] shake for water >> >> Al

Re: [gmx-users] shake for water

> No, it is not the square. > The code does a small 'a' approximation: (1+a)^2=1+2a+a^2 is approx 1+2a. > I have also tested/benchmark shake in gromacs for my first lincs paper > and the plincs paper and it always behaved the way I thought it would. > > The problem is not that you need more iterati

Re: [gmx-users] shake for water

rom: sp...@xray.bmc.uu.se >> To: gmx-users@gromacs.org >> Subject: Re: [gmx-users] shake for water >> >> Berk Hess wrote: >> > >> > >> > > Date: Thu, 5 Feb 2009 19:35:09 +0100 >> > > From: sp...@xray.bmc.uu.se >> > > To: gmx-u

Re: [gmx-users] Free energy perturbation of Cu(I) binding

27;ll need to make sure you explore the energy landscape enough to establish some level of consequence that the preferred state for the protein in the absence of the copper isn't the unfolded state (I'm not talking experimentally, here -- I'm talking about with your particular paramet

Re: [gmx-users] shake for water

ubject: Re: [gmx-users] shake for water >> >> >> >> Berk Hess wrote: >> >> > >> >> > >> >> > > Date: Thu, 5 Feb 2009 19:35:09 +0100 >> >> > > From: sp...@xray.bmc.uu.se >> >> > > To:

[gmx-users] funny zero-step mdrun results in 4.0.3

All, I'm trying to run a zero-step mdrun in 4.0.3 (basically just to evaluate the energy of a specific configuration). I've done this test in 3.3.x and am trying to check if 4.0.3 gives the same energies. I'm also comparing against another simulation package. To this end, I have my starting coordi

Re: [gmx-users] funny zero-step mdrun results in 4.0.3

David, > Both your gro files are wrong, the definition of gro files has never > changed. Do you mean to say this has ever worked? Yes, it worked fine in 3.3.x. I would point out that trjconv has an -ndec option which, if used to output a gro file, will generate high-precision gro files as output.

Re: [gmx-users] funny zero-step mdrun results in 4.0.3

Berk, > I checked the gro manual page: > http://www.gromacs.org/documentation/reference_4.0/online/gro.html > and found out that it is actually pretty clear. > Note that it is fixed format, but with flexible precision which is derived > from the space between the decimal points. Thanks. I was loo

Re: [gmx-users] Re: Free energy with Gromacs.

You may also want to look at www.alchemistry.org, as it has some general information about how these should be set up. On Wed, Mar 18, 2009 at 8:02 PM, Justin A. Lemkul wrote: > > Again, *please keep all Gromacs-related correspondence on the mailing list* >  The type of information that you have

[gmx-users] grompp warnings/errors I haven't seen before

t; mean? Clearly I've got something wrong in my topology or in the relationship between my topology and gro file, but this is not at all transparent. I'll poke around in the source and see if I can figure out what's going on but I thought I might be able

[gmx-users] Re: grompp warnings/errors I haven't seen before

bugzilla with an example input file, I think. It's possible the problem is on my end somewhere, but as far as I can tell I'm not doing anything I'm not supposed to... Thanks, David On Jan 3, 2008 2:33 PM, David Mobley <[EMAIL PROTECTED]> wrote: > All, > > I'm

Re: [gmx-users] topology treatment in free energy calculations - possible bug_2nd

Maik, > It just came to my mind, that the behaviour, I described in the first > mail will be quite dangerous, whenever #define statements are in the > topology, cause this would lead to the insertion of the FF-values in the > topology, when preprocessing, and then be copied into the B-state > afte

Re: [gmx-users] topology treatment in free energy calculations - possible bug

Maik > I just found a strange behaviour of GROMACS, when processing topologies > with B-values. Maybe I just think of it as unintuitive/bug, but here we go: > > e.g. OPLS > > Consider an angle given (all atoms have B-values, which angle-parameter > can be found by GROMACS in the bonded.itp for the

[gmx-users] replica exchange output information

0 .22 .41 .55 .20 .27 .13 .21 I can't find where it's explained what this information means. For example, why are there x's between some numbers and not others? Thanks! David Mobley UCSF http://www.dillgroup.ucsf.edu/~dmobley _

Re: [gmx-users] replica exchange output information

David, > The order is that from low temperature to high temperature (as you could > check from the edr files) and when swaps happen the coordinates and > boxes are exchanged between CPUs. OK. In other words the replicas are always ordered by temperature. > > > > As a follow-up question, is there

Re: [gmx-users] replica exchange output information

I have further replica exchange questions... > >> The order is that from low temperature to high temperature (as you could > >> check from the edr files) and when swaps happen the coordinates and > >> boxes are exchanged between CPUs. > > > > OK. In other words the replicas are always ordered by t

Re: [gmx-users] FEP trajectory errors

r is actually fairly sensitive. This *could* lead to crashes, but I don't know about freezing/vibrating. Let me know if this helps. Best wishes, David Mobley UCSF http://www.dillgroup.ucsf.edu/~dmobley > Can anyone comment on what's going on here? > Thanks, > Bob Johnson > _

Re: [gmx-users] Question Regarding Ligand-Enzyme Complex

For what it's worth, I seem to recall that the ProDrg server itself warns rather strongly about the charges being unreliable, and I definitely agree with Berk here. My favorite approach for modeling small molecules is to use the AMBER GAFF small molecule force field in combination with one of the

Re: [gmx-users] Rugged dG/dlambda when turning off charges

> really isn't any reason to use the soft core potentials when turning > off the charges right? Thus, sc_alpha should be set to zero when > turning off charges? > Thanks, > Bob > > On Jan 25, 2008 5:38 PM, David Mobley <[EMAIL PROTECTED]> wrote: > > It will

Re: [gmx-users] Rugged dG/dlambda when turning off charges

It will only be smooth if you don't use soft core (i.e. sc-alpha =0 ). Best, David Mobley http://www.dillgroup.ucsf.edu/~dmobley On Jan 25, 2008 12:40 PM, Robert Johnson <[EMAIL PROTECTED]> wrote: > Hello everyone, > As I mentioned in a previous post, I'm trying to comput

Re: [gmx-users] dihedral restraints in v3.3 different than v3.3.1 (or broken)

Chris, At one point the forces were incorrrect in the dihedral restraints. I *think* this was in 3.3 but one of the developers will probably know. I have a note to this effect in one of my publications too but I haven't the time to find it right now. David On Jan 26, 2008 10:43 PM, <[EMAIL PRO

[gmx-users] do-dssp

All, I'm using do_dssp to do some secondary structure analysis. I have a peptide with two nonstandard residues, one at the N-terminus and one at the C-terminus, and a total of N residues. The output of do_dssp only contains information on N-2 residues (numbered 1 through N-2) while my trajectory i

Re: [gmx-users] Deviations in free energies with slow growth (single and 3-step process)

Maik, > I simulated a switching process (slow growth TI) over 10ns of ethane to > methanol with hardcore slow-growth in water (365 TIP4P waters,PME) and > in vacuum. The thermodynamic cycle of this calculation yields a DeltaG, > which is in perfect agreement with the experiment and other calculati

Re: [gmx-users] Deviations in free energies with slow growth (single and 3-step process)

col I just don't know. David > Regards > > Maik Goette, Dipl. Biol. > Max Planck Institute for Biophysical Chemistry > Theoretical & computational biophysics department > Am Fassberg 11 > 37077 Goettingen > Germany > Tel. : ++49 551 201 2310 > Fax : ++4

[gmx-users] Re: free energy calculation

this) and get help from someone else on there, or i will be able to attend to it (in that forum) in a few days. Thanks, David Mobley On Feb 11, 2008 5:14 AM, <[EMAIL PROTECTED]> wrote: > Dear david, > i 'm a beginner in molecular dynamics. I was doing the tutorial of md > gro

Re: [gmx-users] Free Energy Calculations

sing > thermodynamic integration to determine my DeltaG values. Bonded parameters > remain untouched. I follow closely the procedure posted by David Mobley at > the > DillGroup Wiki site, changing only a few parameters for my simulation, as I am > using Gromos96, not OPLS-AA. Tha

Re: [gmx-users] Free Energy Calculations

be affected by a bug. It seems like he would have needed to (a) read the entire history of the mailing list, and (b) wade through all of the old bugzillas. Thanks, David On Feb 16, 2008 3:19 PM, David Mobley <[EMAIL PROTECTED]> wrote: > Dear Justin, > > > I'll preface th

Re: 回复： Re: 回复： Re: 回复： Re: 回复： Re: [gmx-users] about using amb2gmx.pl

I think I can probably shed a little bit of light here, although Mark is getting close in the last chapter of his e-mail. Basically, pdb2gmx works well for parameterizing proteins, which the chromophore in question isn't, I'm sure. Since we do lots of protein-ligand simulations, where the ligand i

Re: [gmx-users] Strange dgdl-value together with lincs

Maik, > Assume, you take the interconversion of ethane to methanol in solvent in > one step. > You sample hardcore at 11 evenly spaced lambda values for, lets say, 2 > ns each. > You get the dG/dl mean from every run and integrate via simpson to get a > total DG. Hold on, if you are doing t

Re: [gmx-users] Harmonic dihedral restraints

Robert, I am not sure which manual you are looking at, but in the GROMACS 3.3 manual, equation 4.70 gives the dihedral restraint as harmonic. David On Mon, Feb 25, 2008 at 10:10 AM, Robert Johnson <[EMAIL PROTECTED]> wrote: > Hello everyone, > I am trying to calculate the absolute free energy

Re: [gmx-users] Harmonic dihedral restraints

ok like a harmonic potential in the dihedral angles. Am I just not > seeing something correctly? > Bob > > > > > On Mon, Feb 25, 2008 at 2:47 PM, David Mobley <[EMAIL PROTECTED]> wrote: > > Robert, > > > > I am not sure which manual you are looki

Re: [gmx-users] Free energy of turning on restraints

Bob, > Unfortunately, I'm having problems including the correct restraints in > my topology file. First off, the form of the angle restraint in > Gromacs involves 4 (2 pairs) atoms. The restraint in the Boresch paper > assumes that the angle is between 3 atoms. Is there anyway to apply > the

Re: [gmx-users] ligand-protein interaction using gromacs

Regarding amb2gmx.pl, it should work for converting whole systems from Amber, but this may depend on the box geometry you are using. In particular I think it is OK with cubic boxes but not some of the more fancy geometries. The other option is just to convert your protein+ligand and solvate using g

Re: [gmx-users] Free energy of dihedral restraint

Bob, I don't believe that it is implemented. Developers: It probably should be, since the other restraints can be perturbed. In the interim, it's pretty straightforward to compute the dV/dlambda for restraining from the restraint energy if you know the value of the dihedral angle (which you can e

Re: [gmx-users] average structure with ligand

Be sure to see http://wiki.gromacs.org/index.php/Average_Structure for help interpreting results. On Tue, Mar 18, 2008 at 2:16 AM, Ran Friedman <[EMAIL PROTECTED]> wrote: > Dear Anna, > > Use make_ndx to create any group you find useful. > > Ran. > > > > Anna Marabotti wrote: > > Dear gmx-user

[gmx-users] minimization -- bugzilla or general advice?

All, I often have problems with minimization in gromacs, but now I think I have something a little more systematic to say. First, my system: I am simulating a short peptide in a mix of two co-solvents. I use a program called packmol which can start pack specified number of molecules into a box of

Re: [gmx-users] minimization -- bugzilla or general advice?

Xavier, > I was surprised by the value you use for emstep=1.0e-8. This is the > "maximum step size" and is in nm! I think that's where your problem is. I added this recently in testing because I thought perhaps the problem could be due to using too large of steps. It does not help. So everythin

Re: [gmx-users] minimization -- bugzilla or general advice?

Mark, > However should you find yourself on a very flat area of the PES, then > the smaller the step size, the closer it will look to flat, and thus to > have converged to a stationary point. "Flat" is of course relative to > the step size Right. But of course the problem here has is that

Re: [gmx-users] minimization -- bugzilla or general advice?

Dear Christian, > mmh, just my 0.02€: I guess in a very rough energy landscape (as in > solvated peptides or proteins) this is not generally true, because > with small steps the system might get stuck in the next tiny local > minimum, while with a larger step size it may jump across it. > And

Re: [gmx-users] minimization -- bugzilla or general advice?

Berk, > The problem could be in the constraints. > Gromacs 3 constrains the forces during EM by adding c*f to the coordinates, > constraining those and then dividing the constraint displacement by c. > This limits the accuracy. > > In Gromacs 4 I have implemented force constraining for LINCS and S

Re: [gmx-users] minimization -- bugzilla or general advice?

Berk, > I assume you are using a rigid water model, and thus constraints via SETTLE. Yes, OK. > Constraining is required to measure the size of the force (for convergence > and > step size adjustment) and to make correct steps without enormous extra > displacements in the direction of the force

Re: [gmx-users] minimization -- bugzilla or general advice?

Berk, > Hmm. Is this different from how other packages handle this issue? I > have never had the recurring problems with minimization in GROMACS > that I have in other packages. Even though, strangely enough, water is > a common feature in most of the simulations I run. That was backwards. I

[gmx-users] Re: Free energy

Dear Eudes, I don't have time to provide personalized help with this at present. You'll be better off writing the gromacs forum. You may also want to refer to the general information on performing free energy calculations at http://www.alchemistry.org and previous posts on the gromacs users list.

Re: [gmx-users] Entropy correction in PMF

Chris, I think you are correct here. For binding calculations there is probably a further trick relating to how to define an unbound state that has a well-defined concentration. This I think depends on how one is pulling -- i.e. doing simple radial PMFs is probably a bad idea, because to even conv

Re: [gmx-users] Free energy of discharging and then recharging not zero

Bob, > Hello everyone, > I'm trying to calculate the free energy of binding of DNA bases on a > carbon nanotube. I'm running some tests to make sure that I'm doing > everything correctly. One thing I tried was turning off all the atom > charges of the DNA base and then turning them back on aga

Re: [gmx-users] Free energy of discharging and then recharging not zero

is another matter). Second, the behavior you're describing strikes me as really odd and I think you should get to the bottom of it to make sure there isn't a bug. Hope this helps, David > Bob > > > On Wed, May 7, 2008 at 4:12 PM, David Mobley <[EMAIL PROTECTED]> wrote

Re: [gmx-users] Free energy calculations and speed problems

Yes, what he said. On Mon, May 19, 2008 at 3:00 PM, van Bemmelen <[EMAIL PROTECTED]> wrote: > Hi Justin, > > You shouldn't use PME in vacuo. Just use pbc=no and infinite (i.o.w.: no) > cutoffs. > > I'm not entirely sure why PME takes such a long time, but I can give a very > wild guess. It may hav

Re: [gmx-users] Free energy calculations and speed problems

Justin and Michael, Just to clarify here, I don't think you want the "long cutoff in vacuum" scheme to give you the same results as the "PME in vacuum" scheme. That is, if you use PME in vacuum with a periodic box, you will be including copies of the long-range unscreened electrostatic interaction

Re: [gmx-users] Enthalpy and entropy of binding from thermodynamic integration

Bob, Berk is right. Essentially, it would be easy if we could accurately compute, say, the total enthalpy of our two systems and simply subtract. Unfortunately it's very hard to converge this quantity (basically, subtracting two very large numbers where the error bars are bigger than the differenc

Re: [gmx-users] Re: forward and reverse free energy not consistant (Li Qiang)

Sorry to be slow to chime in here, but there are several reasons one might run into hysteresis, even when not using "slow growth": 1) The aforementioned bug 2) Topology errors 3) Convergence problems. Of 3), there could be many different types. A recurring source of these problems is when people

Re: [gmx-users] mass changes in free energy calculations

You can change the mass if you like. Basically, the net free energy change associated with changing the mass should end up being zero so it will be irrelevant. The mass of course affects the dynamics and things like the velocities, but based on equipartition you can convince yourself that the free

Re: [gmx-users] mass changes in free energy calculations

sk this since I found the forwards and backwards mutation free energy are > more consistant if I do not change the mass. Accidentally? > > LQ > > On Thu, Jun 19, 2008 at 4:26 AM, David Mobley <[EMAIL PROTECTED]> wrote: >> >> You can change the mass if you like. Ba

[gmx-users] hyperthreading

ously can do some benchmarking myself as well but I thought I'd check in with the list first. Thanks so much, David -- David Mobley dmob...@gmail.com 504-383-3662 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archi

Re: [gmx-users] Topology file for D2O

Hi, I am not an expert about heavy water -- but it does seem strange to me to think that you could get "heavy water" just by changing the mass of the hydrogens in a conventional water model. The *only* thing this will affect is the kinetic energy and mass of water. Presumably changing hydrogen to

[gmx-users] tabulated nonbonded interactions and free energy calculations

All, I'm trying to figure out how to use tabulated nonbonded interactions in GROMACS in conjunction with free energy calculations. While the documentation addresses both separately, I am somewhat confused about what would happen if I try to use both simultaneously. In particular, I'm looking at t

[gmx-users] angle-dependent radial distribution function -- documentation problem, or how?

told that the ability is no longer in GROMACS. My question: Is the 3.3 manual in error when it says that g_rdf can do this? If not, how do I use g_rdf in this manner? Thanks, David Mobley ___ gmx-users mailing listgmx-users@gromacs.org http://www.g

[gmx-users] bug in ffoplsaanb.itp?

All, I'm looking at the epsilon value in ffoplsaanb.itp (i.e. from CVS of 3.3.1) for opls_400, F-. It's lilsted as 3.01248e00. This is roughly a factor of 10 larger than many of the other anions (i.e. Cl) and also roughly a factor of 10 larger than the AMBER96 value (in the same units) for F-: 2.

Re: [gmx-users] bug in ffoplsaanb.itp?

Erik and all, No, I don't think so, or at least it's not our typo :-) It is quite common that ions end up with strange radii when you parametrize for free energy of solvation, and in addition those parameters are somewhat old (1984). Here's the extract from Bill Jorgensens file that we translat

Re: [gmx-users] Re: bug in ffoplsaanb.itp?

Alan, Thanks. That's very helpful. I'm actually not using OPLS at all myself -- I just stumbled across this really odd looking set of F- parameters when troubleshooting for someone else. Anyway, your comments are very helpful. I appreciate it. David On 3/31/07, Alan Chen <[EMAIL PROTECTED]> wro

[gmx-users] pairs types for decoupling

All, I'm using the CVS version of 3.3.1 from last week, and am trying to get the new pairs types Berk Hess has implemented to work for doing decoupling. There's an old e-mail here on the subject, which is all I've got to go by: http://www.gromacs.org/pipermail/gmx-developers/2006-March/001530.htm

[gmx-users] modify C6 directly in FF using sigma and epsilon

Gromacs users, I'm using a force field (the port of AMBER to GROMACS) which uses combination rules (combination rule 2), etc. in terms of sigma and epsilon. However, I need to be able to modify C6 directly (in particular, I want to be able to set it to zero). Can anyone give me any pointers on a

Re: [gmx-users] modify C6 directly in FF using sigma and epsilon

David, I'm using 3.3/3.3.1. Is there an easy tweak to the source code that would allow something like this? i.e. could I somehow easily tweak the bit where it reads the nonbond_params section so I can use an alternate combination rule there by specifying, say, a different nonbonded parameter typ

Re: [gmx-users] modify C6 directly in FF using sigma and epsilon

David, It seems that your best bet is to write that little Perl script to convert the whole force field to C6/C12. It's a little worse than that, since I still need to use the same combination rules. I'll have to create a new "force field" where I define all possible pairs of nonbonded interac

Re: [gmx-users] modify C6 directly in FF using sigma and epsilon

st for GROMACS users Subject: Re: [gmx-users] modify C6 directly in FF using sigma and epsilon David Mobley wrote: > David, > > I'm using 3.3/3.3.1. > > Is there an easy tweak to the source code that would allow something > like this? i.e. could I somehow easily tweak

Re: [gmx-users] Re: Ligand_charges

Another possibility is to use a force field which has already been developed for small molecules that makes it easier to parameterize. One example is the Generalized Amber Force Field for small molecules, which can be used with the AMBER protein force fields (which, I might add, have been ported t

Re: [gmx-users] soft-core potential in combination with PME (sorry, again)

Berk and all, I don't understand what David Mobley meant exactly. There is no Coulomb singularity with soft-core. Maybe one could have an unfortunate situation where the LJ is already very soft, but the Coulomb not very soft, which could lead to instabilities. But I have never encountered

Re: [gmx-users] soft-core potential in combination with PME

e meantime I can fix errors in the existing one or clarify. David Greetings, Jeroen > Date: Fri, 13 Apr 2007 09:18:21 -0700 > From: "David Mobley" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] soft-core potential in combination with PME > (sorry, agai

Re: [gmx-users] invalid order for directive position restraints

This usually means the sections in your topology file are not iin the correct order. In particular it is not happy with the order of something in FE.itp, probably the position restraints section. On 4/24/07, S O N A L I <[EMAIL PROTECTED]> wrote: hi everybody, i am working on melenin binding co

Re: [gmx-users] request for dihedral PMF test system or complete alanine dipeptide topology file

Chris, I'll have to assume you know what you're doing with using impropers to calculate PMFs. I've done this using the dihedral restraints code. Have you double-checked that? That's the first place I would look. Otherwise, I don't have a great test system for you. David On 4/25/07, Chris Neal

Re: [gmx-users] request for dihedral PMF test system or complete alanine dipeptide topology file

Chris, I have included my .top file. The relevant section is in [ dihedral_restraints ] This file is a template that I use like this: sed 's/PHI/${phi_value}/' template.top | sed 's/PSI/${psi_value}/' > phi${phi_value}_psi${psi_value}.top Just out of curiousity, which GROMACS version are you

Re: [gmx-users] Request for dihedral PMF test system or complete alanine dipeptide topology file

Chris, >Right. I remember looking into this at one point, and I don't think >the manual is correct; it looks to me like dihres.c handles >periodicity properly. In particular, there is the followign comment in >dihres.c: It's good to see that this is actually a comment in the source code, I didn

Re: [gmx-users] GROMACS Wiki

Erik and all, I think this is a great idea. I've been working on (and plans to work more on) a bit of a free energy wiki/tutorial page beyond what's already available; depending on how this develops I can transfer/combine with what's already on the wiki. As you probably know there are lots of th

Re: [gmx-users] Very large fluctuations in dg/dl

Patrick, My first observation was that 1 ns seemed to be a minimum for certain lambda values (e.g. lambda=0.70). I sometimes read in literature that some authors used a few hundreds of ps, which seemed (to me) not sufficient for proper convergence. My experience is that the range of lambda=0.7

Re: [gmx-users] charge

Hi, I wish to simulate a ligand-protein system..I have used the prodrg server to create the .itp file for my ligand. I have done gaussian charge calculation for my ligand using the chelpg method. how should i incorporate the gaussian charges into my .itp file. should i copy the charges for hea

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