[gmx-users] charge changes in free energy calculations

Dear all, I have a mutation free energy calculation from D(asp) to E(glu). The charge is not changed for the overall mutation. However, following Dr. David Molbey's suggesion, electrostatic and VDW interaction should be modified separately, so in the first step we need to turn off the charge

[gmx-users] Charge change in free energy calculation

Dear all, I have a mutation free energy calculation from D(asp) to E(glu). The charge is not changed for the overall mutation. However, following Dr. David Mobley's suggetion, electrostatic and VDW interaction should be modified separately, so in the first step we need to turn off the charge from

[gmx-users] charge changes in Free Energy calculations

Dear all, I have a mutation free energy calculation from D(asp) to E(glu). The charge is not changed for the overall mutation. However, following Dr. David Mobley's suggetion, electrostatic and VDW interaction should be modified separately, so in the first step we need to turn off the charge from

Re: [gmx-users] charge changes in Free Energy calculations

e CH2 groups? You only have to mind perturbing the bonding and such in the right way then. Cheers, Tsjerk On Sat, Sep 27, 2008 at 6:32 PM, friendli <[EMAIL PROTECTED]> wrote: Dear all, I have a mutation free energy calculation from D(asp) to E(glu). The charge is not changed for

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

atoms that you are going to modify. David On Fri, Sep 26, 2008 at 2:14 AM, friendli <[EMAIL PROTECTED]> wrote: Dear all, I have a mutation free energy calculation from D(asp) to E(glu). The charge is not changed for the overall mutation. However, following Dr. David Molbey&

[gmx-users] oplsaa in Gromacs 4.0

Dear all, Are the topology components of OPLSAA force field explicitly displayed in Gromacs 4.0? I mean the bond, angle, dihedral types(or parameters) following the composed atoms. They are not showed in .top file when oplsaa FF is used, not like other force field, e.g. Gromos96. thanks Qia

[gmx-users] OPLSAA parameters

Dear all, To understand the exact parameters used in oplsaa force field, I read the ffoplsaa*.*** files. But I can not find all the corresponding atom types in the ffoplsaa.rtp and ffoplsaabon.itp files. for example, in rtp file, there is a bond between atom type CG and OG1. But in *bon.itp,

Re: [gmx-users] OPLSAA parameters

[ASN] in ffoplsaa.rtp? thanks Qiang Justin A. Lemkul wrote: friendli wrote: Dear all, To understand the exact parameters used in oplsaa force field, I read the ffoplsaa*.*** files. But I can not find all the corresponding atom types in the ffoplsaa.rtp and ffoplsaabon.itp files. for

Re: [gmx-users] OPLSAA parameters

me atom? what is the difference? Qiang Justin A. Lemkul wrote: friendli wrote: Thank you Justin. Can you tell me how i can find the link between atom names and atom types? That is listed in the .rtp: ; name typechargecgnr CGopls_2350.500 3 The thing I wanna

Re: [gmx-users] OPLSAA parameters

Is that right? why it comes to such complex in GMX? thanks Qiang Mark Abraham wrote: friendli wrote: In ffoplsaa.rtp, I find atom name CG and OG1 corresponds to atom type opls_235 and opls_236. While in oplsaanb.itp, the atom type opls_235 and opls_236 corresponds to atom "name"(as

Re: [gmx-users] OPLSAA parameters

I look at the .top file generated by grompp (-pp). However, for me it is more like a copy of all the force field files into one .top file, so the content are the same as individual ones. Do I miss anything? Thank you Qiang Justin A. Lemkul wrote: friendli wrote: Thank you Justin. Can

Re: [gmx-users] OPLSAA parameters

Hi Mark, the atom types in .top file is opls_???, but the atom types(or "name") in [bondtypes] in ffoplsaabon.itp file is C, H, CT, C_3, etc. So we still need to look up ffoplsaanb.itp to link these two "atom type" (or "name"), right? thanks Qiang Mark

Re: [gmx-users] OPLSAA parameters

Thanks Mark. Hope the developers can consider to output the parameters into .top file explicitly. That would be helpful for mutation calculations at least, I think. Mark Abraham wrote: friendli wrote: Hi Mark, the atom types in .top file is opls_???, but the atom types(or "name

Re: [gmx-users] OPLSAA parameters

ECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] OPLSAA parameters > > Thanks Mark. > > Hope the developers can consider to output the parameters into .top file > explicitly. That would be helpful for mutation calculations at least, I > think. > > >

Re: [gmx-users] OPLSAA parameters

; > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] OPLSAA parameters > > > > > > Thanks Mark. > > > > > > Hope the developers can consider to output the parameters into .top > > file > > > explicitly. That would be helpful for

[gmx-users] print out the velocities and forces using template.c

Dear all users, A silly question: I want to print out the velocities and forces in the trajectories using template.c. In template.c, the coordinates of atom n is in fr.x[n][XX]. Reading the trx.h, i see the x,v and f are defined in the same way. So I just change it to fr.v[n][XX] for velocit

Re: [gmx-users] print out the velocities and forces using template.c

ource of g_traj or trjconv > for examples. > > Cheers, > > Tsjerk > > On Fri, Nov 28, 2008 at 10:33 AM, Mark Abraham <[EMAIL PROTECTED]> > wrote: > > friendli wrote: > >> > >> Dear all users, > >> > >> A silly question:

Re: [gmx-users] print out the velocities and forces using template.c

I think I have found the answer by adding " flags = flags | TRX_READ_V | TRX_READ_F ;". thanks to all. On Sat, Nov 29, 2008 at 12:53 PM, friendli <[EMAIL PROTECTED]> wrote: > I have checked with gmxcheck and velocities and forces are output in .trr. > I am playing temp

Re: [gmx-users] OPLSAA parameters

cs.org > > > > Subject: Re: [gmx-users] OPLSAA parameters > > > > > > > > Thanks Mark. > > > > > > > > Hope the developers can consider to output the parameters into .top > > > file > > > > explicitly. That would be helpful for mutation calcula

[gmx-users] Rugged dgdl curve in turning off/on the charge for Leu

Dear all, When I performing mutation free energy calculation from Leu to Ala, I first turn off the charge on the side chain of Leu. As I read from the GMX archive, the dG/dl curve should be rather smooth for turning off the partial charge. In this step(charge off/on), however, I can not obtai

Re: [gmx-users] Rugged dgdl curve in turning off/on the charge for Leu

thank you for the rational explanation. but is the free energy change in the charge on/off step(~10kJ/mol) small enough to ignore the flucturations? The free energy change in the LJ mutation step is about 8kJ/mol. On Fri, Jan 16, 2009 at 11:56 PM, Jochen Hub wrote: > friendli wrote: >

[gmx-users] free energy decomposition

Dear all, Does Gmx provide the functions to decompose the free energy calculated using TI into various components, such as electrostatic, VDW, covalent or contribution from each residue? If it has, where can I find the procedures to do it? thanks a lot Qiang _

[gmx-users] dgdl convergence in free energy calculation

Dear all, I am calculating the mutation free energies using TI method for a small globulin protein which contains about 40 residues. I meet convergence problems in the FE calculations: (1) when simulations start with different velocities for the some lambda points, the variance of dGdlamba is big

[gmx-users] set up topology in free energy calculations

Dear Gmx users, I am calculating the mutation free energy from amino acid Asp to Asn as a test job for my practice. I have some questions about setting up the topology file. 1, from Asp to Asn mutation, the -CH2-COOH changes to -CH2-CO-NH2 or simply -OH to -NH2. In topology, O <-> N. What ab

[gmx-users] changing mass in free energy calculation

Dear all, I am calculating FE using TI. I have a question about mutating existing atoms with different mass. for example, using ffG53a6 force field, in one case i need to mutate CH2 to CH3, should I use [ atoms ] 17CH3 2ALA CB 6 0 15.035 CH20

[gmx-users] changing mass in free energy calculation

Dear all, I am calculating FE using TI. I have a question about mutating existing atoms with different mass. for example, using ffG53a6 force field, in one case i need to mutate CH2 to CH3, should I use [ atoms ] 17CH3 2ALA CB 6 0 15.035 CH20

[gmx-users] mass changes in free energy calculations

Dear all, I am calculating FE using TI. I have a question about mutating existing atoms with different mass. for example, using ffG53a6 force field, in one case i need to mutate CH2 to CH3, should I use [ atoms ] 17CH3 2ALA CB 6 0 15.035 CH20

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

Hi, I use thermodynamics integration. The protocol is 1000step energy minimization, 20 ps bond-constraint MD, and then 200ps MD for collecting dgdl. thanks Qiang Gerrit Groenhof wrote: Looks like hysteresis. Do you do slow growth, or discrete FEP? Gerrit Dear all Gmxers, I am calcula

[gmx-users] Invitation to connect on LinkedIn

LinkedIn Raymond Friendli requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Raymond Accept invitation from Raymond Friendli http://www.linkedin.