[gmx-users] FEP

Hello all, This is in reply to Michael shirts a while ago on a FEP of a R-CH3 to an R-H group.  Below is the orignal email. I recently tested out mutating a CH3-CH3-(3dummy atoms) molecule on both sides in order to test out that a peturbation would give you a total of 0. forcefield used was

[gmx-users] Slow-growth method question

Hello community, I recently ran several simulations using the g_bar method on several molecule decouplings and I even applied it to some functional group mutations and it seems to work out quite well so far. The only thing is that it requires several simulations to run. I'm attempting to

[gmx-users] Chemical Potential

Hello community, I'm just trying to explore what kind of calculations one can do on polymer systems (pure or in water) in order to validate the force field works accurately for that system. I know there are basics such as density, volume, dH of vaporization, isothermal compressibility, heat

[gmx-users] Re: Chemical Potential

Thank you Jan. -Fabian On Tue, May 22, 2012 at 6:54 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello community, I'm just trying to explore what kind of calculations one can do on polymer systems (pure or in water) in order to validate the force field works accurately

[gmx-users] Determining Force Constants for CG modelling

Hello community, I'm trying to create a topology for a molecule using the MARTINI force field which is a coarse-grain (CG) forcefield. I understand that to optimize the bonded parameters, one needs to model the AA version and extract the equilibrium angle and force constants. As is said in the

[gmx-users] Free Energy of a mutated molecule

Hello all, Please if anybody can help. I'm trying to mutate a -CH3 to an -H (I guess with 3 dummy atoms attached to it). Below I sketched the process. I broke it up into 3 steps and I wanted to use g_bar for the actual mutation step (step 2). Does anybody have any experience with

[gmx-users] decoupling a group of a molecule

Hello, Does anybody know how to do the same decoupling technique from Justin's tutorial but only for a small piece of a molecule rather than the entire molecule? Is it simply writing on the topology B state as zero charge and then mutating to a dummy atom? Thanks. -- Best regards, Fabian F.

[gmx-users] Free Energy tutorial - choosing number of solvent molecules

Hello all, I'm running the same process from the free energy tutorial by Justin Lemkul... http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html . How did the number of solvent particles get chosen (in the tutorial, 210 molecules were chosen)? I seem to

[gmx-users] Re: Free Energy tutorial - choosing number of solvent molecules

and use those as the starting coordinates for a new run? Thanks, Fabian Fabian Casteblanco wrote: Hello all, I'm running the same process from the free energy tutorial by Justin Lemkul...http://www.bevanlab.biochem.vt.edu/Pages

[gmx-users] Noise in a radial distribution function using g_bar

Hello everyone, I'm using radial distribution functions on gromacs for the first time. Is it normal to see some noise on these plots? You can still see a trend on the plot but it appears somewhat noisy and not as nice and linear as some other plots I've seen in other simulations like the

[gmx-users] Noise in a radial distribution function using g_rdf

Sorry, I meant on the previous post, using g_rdf On Mon, Feb 13, 2012 at 12:23 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello everyone, I'm using radial distribution functions on gromacs for the first time.  Is it normal to see some noise on these plots?  You can still see

[gmx-users] Determining energies between a solute and solvent

Hello everyone, Is it possible to see the energy (LJ, Cou) for simply the solute interacting with the solvent? For example, g_energy will calculate all the energies for the entire system interactions which include solvent-solvent interactions. I would simply like the solute-solvent interactions

[gmx-users] Re: Determining energies between a solute and solvent

the simulation. Otherwise, the applicable terms in the .edr file are not decomposed. -Justin On Thu, Feb 23, 2012 at 1:56 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello everyone, Is it possible to see the energy (LJ, Cou) for simply the solute interacting with the solvent

[gmx-users] Re: Determining energies between a solute and solvent

know how to do this using make_ndx for g(r) plots but I don't see how you can apply it to energygrps on the *.mdp file. Thanks again for all your help. -Fabian On Thu, Feb 23, 2012 at 2:41 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Thanks.   So before I run the simulation, I

[gmx-users] Radial distribution function by COM

Hello everyone, Is there any way to do a g(r) plot between the COM of a single solute particle, and the COMs of each solvent molecule around it? It seems to only let your choice be the COM for the first pick. Is there any way to do it for both choices? Thanks. -- Best regards, Fabian F.

[gmx-users] couple-moltype question

Hello Gromacs community, I am trying to simply decharge a part of large molecule. I know from the tutorial we can use 'couple-moltype' along with 'couple-lambda0', etc, but in this case I simply change the topology to state A and then I have state B written with no charges since I'm only doing a

[gmx-users] Potential energy methanol in a box

Hello, I'm trying to fill a box with methanol using CHARMM FF Parameters.  I also need to do this for ethanol and 1-propanol. For ethanol, each individual molecule had approximately -19 kJ/mol of potential energy, then I placed 1000 in a box, performed nvt, npt, etc.  End Result:  A negative

[gmx-users] Re: Potential energy methanol in a box

Thanks again for your response. I appreciate all your help. On Sat, Apr 23, 2011 at 6:11 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello, I'm trying to fill a box with methanol using CHARMM FF Parameters.  I also need to do this for ethanol and 1-propanol. For ethanol

[gmx-users] Unsteady Density

Hello, I have been trying to use CHARMM forcefield to simulate 1000 molecules of Methanol in a box but I seem to fall short on the density every time I run. At first, I had my rlist at 1 but CHARMM recommends greater than 1.2-1.4 nm so I changed accordingly, then I changed it so that the short

[gmx-users] Re: Unsteady Density

. On Mon, May 2, 2011 at 2:16 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello, I have been trying to use CHARMM forcefield to simulate 1000 molecules of Methanol in a box but I seem to fall short on the density every time I run.  At first, I had my rlist at 1 but CHARMM recommends

[gmx-users] Re: Unsteady Density

. On Mon, May 2, 2011 at 2:16 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello, I have been trying to use CHARMM forcefield to simulate 1000 molecules of Methanol in a box but I seem to fall short on the density every time I run.  At first, I had my rlist at 1 but CHARMM

[gmx-users] Genbox question

Hello, I was wondering if someone can help me with a general genbox question. I have been using the command line: genbox -ci octanol.gro -nmol 1000 -box 5 5 5 -o prop_1000.gro to fill a box with 1000 molecules of octanol. With the smaller n-alcohols, it worked fine but as I started using

[gmx-users] Enthalpy of vaporization

Hello all, I am trying to find the enthalpy of vaporization for 7 types of alcohols to try to compare to experimental values. I have all of them simulated to equilibrium and I can use g_energy to view the Total Energy (both kinetic and potential). In order for me to find the enthalpy of

[gmx-users] Enthalpy of Vaporization

Hello Justin, Thank you for your response. I just wanted to make sure I understand what you meant. I'm assuming that you want the one molecule in the gas phase at its boiling point and you are doing this because you want the molecule alone with no intermolecular interactions? (since heat of

[gmx-users] Enthalpy of Vaporization

Thanks Justin. That clarified a lot. I'm having trouble simulating the 1 molecule of gas methanol. I took the original energy minimized molecule and I'm trying to start it off on NVT using the following *.mdp file. I got rid of PBC (ns_type=simple) and I set rlist=infinite. After correcting

[gmx-users] Enthalpy of Vaporization

Thanks Justin. It worked and it is only off by 3% from experimental value so that is great. Thanks for your help! -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E:  fabian.castebla...@gmail.com -- gmx-users mailing list

[gmx-users] Liquid/Gas Systems

Hi Justin, You had helped me earlier on calculating the heat of vaporization of methanol and it worked great. I'm just trying hard to understand conceptually what is the difference between simulating a liquid phase and a gas phase in Gromacs. I mean technically if we throw in 1000 molecules of

[gmx-users] Heat Capacity Question

Hello, I am trying to compare the heat capacity (at NPT) of 1000 molecules of methanol. I ran it all to equilibrium and used g_energy and -nmol 1000 to calculate the heat capacity. The value I achieved, ~140 J/mol*K is far from what I see is 79.5 J/mol. I have read on some past posts that

[gmx-users] Using new atom types

Hello all, I'm building a drug molecule using CHARMM parameters. The thing is that there is this new CGenFF (an extension of CHARMM, but very similar to the old CHARMM atom types http://mackerell.umaryland.edu/~kenno/cgenff/) that uses better parameters for drug-like molecules. I would like to

[gmx-users] Re: Using new atom types

access to change internal files. I do not need to run using pdb2gmx. Also, how did you manage to include the LJ 1-4 parameters? Did you have to write out each and every pair on GROMACS? Thanks for you help. -Fabian On Thu, Jul 7, 2011 at 2:16 PM, Fabian Casteblanco fabian.castebla...@gmail.com

[gmx-users] Re: Using new atom types

charmm27.ff/forcefield.itp **???{ #include add new CgenFFbon.itp and CgenFFnb.itp here? }???**? #include drug.itp [ system ] ; Name DrugName [ molecules ] ; Compound#mols DDD 1 Thanks again for your help. Greatly appreciated!! Fabian Casteblanco Rutgers

[gmx-users] vdW cutoff

Hello, I am quite confused on whether it is better to use a standard cut-off scheme for vdW interactions or if its better to use a switch or shift function for this. I am doing a free energy calculation on the solvation of a drug molecule in a solvent (on CHARMM ff) so I want to be as accurate

[gmx-users] Dihedral Question

Hello all, I'm having trouble finding information that explains the relationship between 1,4 pair interactions and dihedrals. I'm building a drug molecule using CGenFF, and extension of CHARMM27 and since the drug is a bit complex, it has several dihedral parameters that are missing. I ran them

[gmx-users] Re: Dihedral Question

Thanks Justin for your help :-) Best regards, Fabian Casteblanco On Fri, Aug 5, 2011 at 11:46 AM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello all, I'm having trouble finding information that explains the relationship between 1,4 pair interactions and dihedrals.  I'm building

[gmx-users] Free energy calculation

Hello all, I am setting up a free energy calculation (drug from full coulomb+vdW in solution -- drug with only vdW in solution -- dummy drug in solution). After reading most of the papers, I understand that you need significant overlap from the energies for each intermediate point to overlap so

[gmx-users] Re: Free energy calculation

Thanks Justin. Best regards, Fabian On Mon, Aug 8, 2011 at 5:49 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello all, I am setting up a free energy calculation (drug from full coulomb+vdW in solution -- drug with only vdW in solution -- dummy drug in solution). After

[gmx-users] Free_energy size selection

Hello all, I'm running a free energy simulation using BAR method for a one drug molecule in several alcohols. I started off using 500 solvent molecules for but realized it was taking too long for the smaller solvents, which would make the larger solvents even more time consuming. I reduced it

[gmx-users] Free Energy Integrator Selection

Dear all, I was running free energy calculation for a drug molecule in solvent. First, For [coulomb + vdW] -- [vdW] ,  I used 'md' integrator For [vdW] -- [none], I was using 'md' but it required me to switch to 'sd' based on this error message: WARNING: For proper sampling of the (nearly)

[gmx-users] Convert drug Charmm topology to Gromacs

Hello Steven Neumann, I recently converted CGenFF parameters into files that are used by Gromacs. If this is what you need, shoot me an email and I can provide you with the data sets. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723

[gmx-users] Re: Convert drug Charmm topology to Gromacs

Hello Dr. Alexandre Suman de Araujo, I am not sure how to upload to Gromacs User Contribution. I see downloadable files but not place to upload. Do you have the link where I can upload the files? Thanks, Fabian On Wed, Aug 24, 2011 at 2:55 PM, Fabian Casteblanco fabian.castebla...@gmail.com

[gmx-users] Free energy calculation question

Hello Justin, I'm calculating the free energy of a drug in an alcohol solvent.  I have a question referring to your free energy tutorial.  You mentioned that decoupling of electrostatic interactions is linear and decoupling of vdW can vary.  Is this true for your case of methanol in water or for

[gmx-users] Re: Free energy calculation question

different amount of solvent molecules and using MD and SD integrator) and they all seem to be giving similar results. Thanks for your help. -Fabian On Wed, Aug 31, 2011 at 11:24 AM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello Justin, I'm calculating the free energy of a drug

[gmx-users] Re: Free energy calculation question

to increase this ;value to 100 for your own work. ;Velocity generation gen_vel =no ;Velocity generation is off ;END On Wed, Aug 31, 2011 at 11:24 AM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello Justin, I'm calculating the free

[gmx-users] Re: Free energy calculation question

Thanks Justin! On Wed, Aug 31, 2011 at 11:24 AM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello Justin, I'm calculating the free energy of a drug in an alcohol solvent.  I have a question referring to your free energy tutorial.  You mentioned that decoupling of electrostatic

[gmx-users] Free energy sampling using G_bar

Hello all, I am finished running a free energy calculation using g_bar and i followed Justin Lemkuls tutorial and I am in the process of analyzing inorder to determine if I had adequate sampling.  I have read the 'BAR' paper by Bennett but there are still some concerns whether I have enough

[gmx-users] Free Energy Question

Hello all, I have a general question about calculating free energies. I recently used g_bar to calculate the free energies of decoupling coulombic and vdW forces of a solute molecule in solvent. I now need to calculate the free energy of a solute molecule mutating to a new molecule (identical

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

Hello Justin, I have a question about your tutorial. If I want to mutate one small group of a molecule, I would have to not provide 'couple_lambda0' and 'couple_lambda1', correct? I would essentially have to follow sec 5.7.4 in the Gromacs manual and I have to actually provide all state A

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

Thank you guys for your help. I appreciate it. On Thu, Oct 6, 2011 at 1:05 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello Justin, I have a question about your tutorial.  If I want to mutate one small group of a molecule, I would have to not provide 'couple_lambda0

[gmx-users] FEP

Hi all, I have an additional question related to what Steven Neumann was mentioning. I actually have to do a molecule mutation. I'm trying to use Michael Shirts method 1) making small changes 'alchemical' changes in the molecules and computing the free energies by any method (BAR, TI, etc).

[gmx-users] Re: FEP

Thanks Michael for your help. This really helps a lot. Thank you! On Mon, Oct 10, 2011 at 4:10 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hi all, I have an additional question related to what Steven Neumann was mentioning.  I actually have to do a molecule mutation.  I'm

[gmx-users] Re: FEP

. Does anybody have any experience with this? Thank you for your help. -Fabian Casteblanco Portion of Error Output: - Reading file nvt0.5.tpr, VERSION 4.5.3 (single precision) starting mdrun 'SIMVASTATIN' 15 steps,300.0 ps

[gmx-users] Peturbing a Dihedral for FEP

it to run.  Does anybody have any experience with this? Thank you for your help. -Fabian Casteblanco Portion of Error Output: - Reading file nvt0.5.tpr, VERSION 4.5.3 (single precision) starting mdrun 'SIMVASTATIN' 15 steps

[gmx-users] Mixing Force Fields

Hello community, I have a general question about mixing force fields. I want to try to use CGenFF to model the drug and I wanted to use CHARMM for the solvent. I see the general advice given online is to always use only one forcefield but I know CGenFF was developed off CHARMM but specifically

[gmx-users] Pressure coupling problem

Hi, I'm still in my first few months of using Gromacs. I started by creating an *.itp and *.top file for *Ethanol* using CHARMM force field parameters. I made the molecule and it looked fine, put 1000 molecules in a box, energy minimized it to a negative potential energy, viewed it on VMD,

[gmx-users] Pressure coupling problem

Hi, I'm still in my first few months of using Gromacs.  I started by creating an *.itp and *.top file for Ethanol using CHARMM force field parameters.  I made the molecule and it looked fine, put 1000 molecules in a box, energy minimized it to a negative potential energy, viewed it on VMD, again

[gmx-users] Pressure coupling problem

. Thanks. On Mon, Apr 11, 2011 at 4:55 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hi, I'm still in my first few months of using Gromacs. I started by creating an *.itp and *.top file for *Ethanol* using CHARMM force field parameters. I made the molecule and it looked fine, put

[gmx-users] Genbox command question

Hello, I'm trying to place 1000 molecules of 1-propanol using CHARMM FF parameters in a -box 6 6 6.   After minimization, I realized that for a single molecule, the potential was slightly above 0, '+24 kJ/mol' to be exact, with electrostatic coloumb potential the greatest contributor.  I used the

[gmx-users] Re: Genbox command question

Thank you Justin. Your explanation really helped. I was actually using 4.0.5, not 4.0.1 (my mistake). Your explanations explained everything very well. Thanks again for your help! On Fri, Apr 15, 2011 at 3:33 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello, I'm trying