[gmx-users] where are GB parameters stored?

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...@gmail.com 504-383-3662 -- gmx-users

Re: [gmx-users] Regarding free energy calculation

and Hunenberger papers from J. Chem. Phys (2006 or 2007) and references therein. The good news is that for simple spherical ions KH 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 at 6:41 AM

[gmx-users] dihedral restraints documentation

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.gromacs.org

Re: [gmx-users] FEP charged molecule cuestion

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-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

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

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-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] hyperthreading

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 archive at http

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

SUNITA GUPTA 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 archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use

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

...@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. These questions are better put on the GROMACS users list. 1) Yes

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

? Peter Nagy The University of Toledo -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

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 ckut...@gwdg.de 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

[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,

[gmx-users] Fwd: fixed 3.3.3?

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 dlmob...@uno.edu Office 504-280-6445 Fax 504-280-6860

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 jalem...@vt.edu wrote: Again, *please keep all Gromacs-related correspondence on the mailing list*  The type of information

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 looking

Re: [gmx-users] shake for water

-users@gromacs.org Subject: Re: [gmx-users] shake for water David Mobley wrote: 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

[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

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 All, A quick

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 iterations

Re: [gmx-users] shake for water

-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@gromacs.org Subject: Re: [gmx-users] shake for water David Mobley wrote: All, A quick question on constraints... I'm using TIP4P-Ew in gromacs

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

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 parameters). David Mobley, Ph.D. Assistant Professor of Chemistry University of New

[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] 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

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

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 always had

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

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 of Chemistry University of New

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

you to check your own studies that have used TIP4P/TIP4P-Ew and see if they are affected. David Mobley Assistant Professor Department of Chemistry University of New Orleans ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

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 on all

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

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 504-280-6860 Thanks, Chris. -- original message -- Eudes

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

From: David Mobley dmob...@gmail.com Subject: Re: [gmx-users] Free energy of transfer with accuracy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: bc2c99750812110524r1aee080av4ac07eed79b4b...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi

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

?) 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 which you're doing so we can help better. David Mobley, Ph.D. Assistant Professor of Chemistry University of New Orleans New Orleans, LA

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 before

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

, 11 Dec 2008 07:24:26 -0600 From: David Mobley [EMAIL PROTECTED] Subject: Re: [gmx-users] Free energy of transfer with accuracy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Hi, Hi gmx-users

[gmx-users] off topic: graduate school opportunity

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 70148

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

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

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. Basically, the net free energy change associated with changing the mass

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] 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

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 interactions

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 have

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

at 4:12 PM, David Mobley [EMAIL PROTECTED] wrote: 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

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 again.

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

[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] 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

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] 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

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 everything I

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 the

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 I

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

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

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] Harmonic dihedral restraints

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 looking at, but in the GROMACS 3.3 manual, equation 4.70 gives the dihedral restraint as harmonic. David

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 of

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 this

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

Re: [gmx-users] Free Energy Calculations

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. Thanks. This is a good intro -- helps to know what level of help

Re: [gmx-users] Free Energy Calculations

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 this message by saying that this is my first foray into free

[gmx-users] Re: free energy calculation

on 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 group, hydration free energy

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

: mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ David Mobley wrote: 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

[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

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

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

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 only be smooth if you don't use soft core (i.e. sc-alpha =0 ). Best, David Mobley http

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

Re: [gmx-users] FEP trajectory errors

-alpha = 0.7 can lead to a fairly steep dV/dlambda and some large forces near lambda=1, which is why I recommend sc-alpha = 0.5. This parameter 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

[gmx-users] replica exchange output information

.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 ___ gmx-users

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 an

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 temperature.

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

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 A-

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

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 to expedite things by an e-mail to the list. Thanks, David Mobley http://www.dillgroup.ucsf.edu/~dmobley

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

a 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 trying to simulate a peptide/water/cosolvent

[gmx-users] opls parameters in distribution

a viable option. Thanks, David Mobley ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe

Re: [gmx-users] how to deduce charges for gromos forcefield?

Probably the easiest way for you to get an answer to this is to look up the references which discuss the parameterization of the GROMOS force field. Consistency is the name of the game. See here: http://wiki.gromacs.org/index.php/Parameterization David On Nov 25, 2007 1:21 AM, Q733 [EMAIL

Re: [gmx-users] Adding polarizability

David, As Mark answered there is no out of thebox polarizability. AFAIK there is no complete force field like that in Amber either, only Tinker has one. Just to clarify here, AMBER has an implementation of AMOEBA, Jay Ponder's polarizable force field that is also implemented in Tinker. So yes,

Re: [gmx-users] Adding polarizability

David, Interesting, does that include all the multipoles and buffered 7-14 potentials etc? Yes. My understanding is that the implementation is somehow separate from the main AMBER implementation and actually requires a copy of Tinker to set up the input files, but this may have changed (I

Re: [gmx-users] restart an amber run in gromacs

Hi, servaas michielssens wrote: I used amb2gmx.pl (from http://chemistry.csulb.edu/ffamber/) to convert an amber topology and restart file to a gromacs topology and structure file and tried to continue the simulation in gromacs. I got the following error message: Constraint error in

Re: [gmx-users] How to delete bad water molecules

Chris, I don't know the answer to the exact question that you have posed, but I instead suggest that getting rid of that water molecule is not a good idea. You should rather minimize your system. While minimizing, be sure to include define=-DFLEXIBLE in your .mdp file Just out of

Re: [gmx-users] soft-core and coulomb transformation

Nov 2007, David Mobley wrote: Dear Bharat, OK, I went ahead and ran with your topologies using my own run scripts. My runs haven't finished yet, but looking at just dV/dlambda values from equilibration, I seem to be seeing roughly the same trends you do. In particular: (1

Re: [gmx-users] soft-core and coulomb transformation

). Bharat, be sure you submit a bugzilla and we'll see how things go from there. I may at some point try setting up some of my own relative free energy topologies and see if I see the same effects, but I'm not likely to have time for that for a couple days. Thanks, David On 11/12/07, David Mobley

Re: [gmx-users] soft-core and coulomb transformation

versus discharging is that charging is where the A state has zero charges and the B state has normal charges, and discharging is the reverse. So charging is the scenario you describe, and discharging is the reverse. David Berk. From: David Mobley [EMAIL PROTECTED] Reply-To: Discussion list

Re: [gmx-users] soft-core and coulomb transformation

Bharat, Your values for the first set of calculations (the forward case?) below look really weird. I suspect you have something messed up in those runs. Have you checked that your define statements worked properly, and checked your run input files? In particular, your dv/dlambda is staying almost

[gmx-users] Ace-Ala-Nac to Ace-Gly-Nac

Dear Bharat, OK, I went ahead and ran with your topologies using my own run scripts. My runs haven't finished yet, but looking at just dV/dlambda values from equilibration, I seem to be seeing roughly the same trends you do. In particular: (1) The forward simulation always gives dv/dlambda

Re: [gmx-users] Re: mdrun -rerun and box size bug not fixed?

Hi, By reactivating the barostat as mentioned below, I managed to recover LJ energies within 0.1% for my test system, which was a box of 1136 waters. So I applied the same thing to my system of interest (a 605 residue protein with around 25000 waters). The only difference is that the run was

Re: [gmx-users] soft-core and coulomb transformation

Hi, Everything goes fine till this point. Now, i do reverse transformations to check for hysteresis. For vdw transformations, i get almost perfect overlap of dG/dlambda vs lambda for forward and reverse transformations, but for coloumb transformations, if i don't use soft-core potentials, i

Re: [gmx-users] soft-core and coulomb transformation

Hi, it is fairly straight FORWARD.. forward is from state A to state B, and reverse is from state B to state A. Say for example, forward transformation is going from ethane to methane. in this step, i define three of the terminal hydrogen on say C2, with zero charges and C2 with charge of

Re: [gmx-users] soft-core and coulomb transformation

Hi, i am extremely sorry here.. i am plotting dg/dl vs lambda of reverse transformation onto that of forward with both axes reversed. so i should expect overlap. this is consistent with whatever you are saying. i am sorry for negligence and confusion. And taking the negative? but when i

Re: [gmx-users] mdrun -rerun and box size bug not fixed?

Dear Michel, Are you sure you're using 3.3.1? I have not checked this specific issue -- but I have checked that if I run hydration free energy calculations in patched 3.3.0, and again in patched 3.3.1, and do my usual free energy analysis using mdrun -rerun, I get the same values. That either

Re: [gmx-users] potential energy of only the protein

Hi, Depends on what you mean by the potential energy of only the protein. The protein alone in what environment? (And what do you hope this will tell you?) One thing you can do -- assuming this is what you want to do -- is strip out all of the waters and then use mdrun -rerun to evaluate the

Re: [gmx-users] langevin dynamics

Just my unasked-for two cents: Langevin dynamics in water is probably a poor substitute for some representation of water. Langevin can provide some of the friction/noise of water -- but electrostatics interactions are very different in water than in vacuum. Langevin dynamics is probably not a

Re: [gmx-users] thermodynamic integration

Hi, is it possible to do thermodynamic integration in Gromacs using non-linear scaling of the lamda paramerter? I'm not sure exactly what you mean, so first I'll answer what I think you mean, and then tell you what I think you ought to be asking. :) If you mean, Is it possible to perform a

Re: [gmx-users] forcefield validation

Hi, Many articles didn't give out the validation procedure of their topologies in detail, are there some classic articles explaining how the forcefield we used today, such as OPLS, GROMOS, AMBER and CHARMM , developed? I want to know how they were deduced from the very beginning. There is

Re: [gmx-users] forcefield validation

First, thanks very much for your instruction. If quantum chemical calculation does not have any physical meaning, how should I decide the partial charge for a molecule? David is correct, he was referring to Mulliken charges. Again, there is no *right* answer to this, the name of the game is

[gmx-users] weird problem on small molecules with triple bonds

All, I may be in a hole of my own digging, here, but I've been trying to simulate a large set of small molecules in explicit solvent. I'm using the Amber GAFF parameters, converted over to GROMACS using our amb2gmx.pl script. The problem I'm running into is that for anything with a triple bond

Re: [gmx-users] forcefield validation

Alan Dodd's suggestion is nice, but there isn't always a lot of experimental data available for a particular molecule we can compare with -- or perhaps we want to begin with good parameters and then see if our method can reproduce experiment. Anyway, for whatever reason it isn't always possible to

Re: [gmx-users] weird problem on small molecules with triple bonds

David, On 10/16/07, David van der Spoel [EMAIL PROTECTED] wrote: David Mobley wrote: All, I may be in a hole of my own digging, here, but I've been trying to simulate a large set of small molecules in explicit solvent. I'm using the Amber GAFF parameters, converted over to GROMACS

[gmx-users] problem with linear molecules and suggested fix

, David Mobley UCSF http://www.dillgroup.ucsf.edu/~dmobley ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un

[gmx-users] Re: FEP problem

Dear Qin, I believe the GROMACS manual recommends doing constant volume equilibration prior to doing constant pressure equilibration. This is what I always do. My understanding is that the Berendsen barostat tends to be rather picky and crash (as you're seeing) when the system is changing

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