Re: [gmx-users] filling a mesopore with water

Hi Chaban, they are less than 5 Angstrom. On Tue, Jun 23, 2015 at 1:30 AM, V.V.Chaban wrote: > what's the size of the hole? > > > > > On Mon, Jun 22, 2015 at 11:37 AM, Maryam Kowsar > wrote: > > Dear users, > > > > I want to fill a mesoporous system with water or any other molecules or > > ato

Re: [gmx-users] gas phase force field

hello, Thanks for yours valuable comments, So Which force fields do you people recommend to simulate gas phase systems?Can we simulate gas and liquid mixtures in one go? RegardsSwapnil On Monday, 22 June 2015 6:26 PM, Justin Lemkul wrote: On 6/22/15 8:47 AM, V.V.Chaban wrote: >

Re: [gmx-users] Re; .xtc and .trr file is missing

On 6/22/15 9:47 PM, RJ wrote: Dear Tsjerk, I already set " nstxout-compressed = 5000 ; write .xtc trajectory every 10.0 ps " in my mdp file Confirm the settings in the .log file. My cpt file checking through gmxcheck are reading the 100 ns as last frame but dont how i miss this .x

[gmx-users] Re; .xtc and .trr file is missing

Dear Tsjerk, I already set " nstxout-compressed = 5000 ; write .xtc trajectory every 10.0 ps " in my mdp file My cpt file checking through gmxcheck are reading the 100 ns as last frame but dont how i miss this .xtc and .trr file? It could happen lack of memory ? Any possible to get those

Re: [gmx-users] filling a mesopore with water

what's the size of the hole? On Mon, Jun 22, 2015 at 11:37 AM, Maryam Kowsar wrote: > Dear users, > > I want to fill a mesoporous system with water or any other molecules or > atoms. I tested genbox -cp .gro -cs spc216.gro -o but water molecules only > surround the mespore not in the holes. Ar

Re: [gmx-users] Get pdb2gmx not to treat the first nucleotide in a chain as 5'

Hi, On Mon, Jun 22, 2015 at 8:50 PM Peter Stern wrote: > Even though it's called aminoacids.n.tdb? Or a different name, e.g. > nucleicacids.n.tdb? > One problem is that I eventually have to deal with tens, maybe hundreds of > complexes. > Some, of course, will have the normal 5' nucleotide. Wi

Re: [gmx-users] installation errors

Hi, The solution suggested by Parvez should work, but really you should not install this version of GROMACS any more (at least get the bug fixes in 4.5.7!) and should do so only after reading the install instructions on the GROMACS webpage, which deal specifically with the issue you report. Mark

Re: [gmx-users] Get pdb2gmx not to treat the first nucleotide in a chain as 5'

Peter, it should be in aminoacids, just a legacy file naming. Alex On Mon, Jun 22, 2015 at 12:46 PM, Peter Stern wrote: > Even though it's called aminoacids.n.tdb? Or a different name, e.g. > nucleicacids.n.tdb? > One problem is that I eventually have to deal with tens, maybe hundreds of > com

Re: [gmx-users] Get pdb2gmx not to treat the first nucleotide in a chain as 5'

Even though it's called aminoacids.n.tdb? Or a different name, e.g. nucleicacids.n.tdb? One problem is that I eventually have to deal with tens, maybe hundreds of complexes. Some, of course, will have the normal 5' nucleotide. Will I be able to choose the appropriate n.tdb file for each case

Re: [gmx-users] installation errors

Thanks Parvez! but it was not the solution. do you have any other ideas to help? On Sun, Jun 21, 2015 at 1:42 PM, mah maz wrote: > Dear all, > I am trying to install a new version of gromacs(rather than rpm) on my > system. I apply these commands:(in root while im superuser) > tar -xzvf fftw-3.3

Re: [gmx-users] Get pdb2gmx not to treat the first nucleotide in a chain as 5'

On 6/22/15 2:36 PM, Peter Stern wrote: I have a chain of RNA in complex with a protein. The pdb file is missing the first two nucleotides and starts with the third including the PO2 group. pdb2gmx identifies this as the 5' terminal nucleotide and tries to create the topology from rna.rtp usin

[gmx-users] Get pdb2gmx not to treat the first nucleotide in a chain as 5'

I have a chain of RNA in complex with a protein. The pdb file is missing the first two nucleotides and starts with the third including the PO2 group. pdb2gmx identifies this as the 5' terminal nucleotide and tries to create the topology from rna.rtp using RA5 as the "residue" type. Thus it doesn

Re: [gmx-users] md-vv and md

Hi Michael, There is one more question, I still could not get why do I see that big jump in potential energy? I understand all bulk is drifting in the box because of the COM removal step is omitted for md-vv but how this issue can effect the potential energy? best On Mon, Jun 22, 2015 at 4:05 PM

[gmx-users] Fatal error: You selected groups with differen number of atoms.

Hi All I want to align small residues based on 3 atom names only (ignoring rest of the atoms) and confrms does not require same number of atoms: first.pdb with 7 atoms and second.pdb with 3 atoms. echo "0" "0"| gmx confrms -f1 first.pdb.pdb -f2 second.pdb -no -name -o fit.pdb I am getting error

[gmx-users] filling a mesopore with water

Dear users, I want to fill a mesoporous system with water or any other molecules or atoms. I tested genbox -cp .gro -cs spc216.gro -o but water molecules only surround the mespore not in the holes. Are there any commands in gromacs? thank you. -- Gromacs Users mailing list * Please search the a

Re: [gmx-users] md-vv and md

Thanks Michael. On Mon, Jun 22, 2015 at 3:50 PM, Michael Shirts wrote: > At some point, a COM removal step was omitted for md-vv. A change has been > proposed in in gerrit for a while (See > https://gerrit.gromacs.org/#/c/4649/ > and https://gerrit.gromacs.org/#/c/4467/ ), but one of the develo

Re: [gmx-users] md-vv and md

At some point, a COM removal step was omitted for md-vv. A change has been proposed in in gerrit for a while (See https://gerrit.gromacs.org/#/c/4649/ and https://gerrit.gromacs.org/#/c/4467/ ), but one of the developers asked to have the source of the problem traced to understand better what happ

[gmx-users] REMD mdrun_mpi error

Dear gromacs users, I am trying to simulate a ligand using REMD method in explicit solvent with the charmm force field. When I try to equilibrate my system I get this error : Double sids (0, 1) for atom 26 Double sids (0, 1) for atom 27 Double sids (0, 1) for atom 28 Double sids (0, 1) for atom 2

[gmx-users] md-vv and md

Hi all, I was using md-vv as an integrator however I discovered that all bulk was moving (drifting) during the simulation. Than I changed the integrator and used md. The bulk molecules did not move during the simulation, just stayed in the middle of box. I attached the potential and kinetic ene

Re: [gmx-users] gas phase force field

On 6/22/15 8:47 AM, V.V.Chaban wrote: Not all organics is polar, Justin. :-) Obviously. Hydrogen bond length, and hence, energy are well limited by sigma in LJ. Even if dipole moments are overestimated by 20%, this should not lead to a proportional increase in the hydrogen bond strength.

Re: [gmx-users] gas phase force field

Not all organics is polar, Justin. :-) Hydrogen bond length, and hence, energy are well limited by sigma in LJ. Even if dipole moments are overestimated by 20%, this should not lead to a proportional increase in the hydrogen bond strength. On Sun, Jun 21, 2015 at 9:52 PM, Justin Lemkul wrote

Re: [gmx-users] temperature problem

Thanks Justin Regrads Lovika On Mon, Jun 22, 2015 at 6:11 PM, Justin Lemkul wrote: > > > On 6/22/15 7:55 AM, Lovika Moudgil wrote: > >> Hi everyone >> >> Can anybody tell from where I will get this tip3p.gro file ...I have >> tip4p.gro and tip5p.gro ...but not tip3p.gro >> E

Re: [gmx-users] temperature problem

On 6/22/15 7:55 AM, Lovika Moudgil wrote: Hi everyone Can anybody tell from where I will get this tip3p.gro file ...I have tip4p.gro and tip5p.gro ...but not tip3p.gro Error is :: *Library file tip3p.gro not found in current dir nor in default directories.(You can set the direct

Re: [gmx-users] Free energy calculation

On 6/22/15 7:10 AM, nazli kashani javid wrote: thanks for your clear answer. Is there any reasonable method for calculating free energy of solvation for my protein? :-( Try MM/PBSA or MM/GBSA calculations. -Justin -- == Justin A. Lemkul, Ph

Re: [gmx-users] Hessian Matrix Order

Hi Eugen, It's indeed x1,y1,z1,x2,y2,z2,...,xN,yN,zN Cheers, Tsjerk On Thu, Jun 18, 2015 at 9:59 PM, Command Line wrote: > Hi, Does some know the exact order of the hessian matrix elements? > There are 3N x 3N elements, which match up with the N atoms. > But I'm not sure how the x, y, z eleme

Re: [gmx-users] temperature problem

Hi everyone Can anybody tell from where I will get this tip3p.gro file ...I have tip4p.gro and tip5p.gro ...but not tip3p.gro Error is :: *Library file tip3p.gro not found in current dir nor in default directories.(You can set the directories to search with the GMXLIB path variable)

Re: [gmx-users] Free energy calculation

I'm trying to show thermodynamic stabilities of my protein from free energy simulation. And I chose free energy of solvation, so if I can't use this method how can I show thermodynamic stabilities of my protein? On Mon, Jun 22, 2015 at 3:40 PM, nazli kashani javid wrote: > thanks for your clea

Re: [gmx-users] Free energy calculation

thanks for your clear answer. Is there any reasonable method for calculating free energy of solvation for my protein? :-( On Mon, Jun 22, 2015 at 2:26 PM, Justin Lemkul wrote: > > > On 6/22/15 5:53 AM, nazli kashani javid wrote: > >> Dear all >> >> I'm trying to calculate free energy of sol

Re: [gmx-users] Free energy calculation

On 6/22/15 5:53 AM, nazli kashani javid wrote: Dear all I'm trying to calculate free energy of solvation according to Justin's tutorial for my protein in water. Is it true to follow that tutorial for my protein? any special changes in MDP file is necessary ? You shouldn't use this method a

Re: [gmx-users] membrane model

If you check out the second paper I linked to before ( the shameless plug to my own work!), this should give you a good idea. That said, this work is a from a few years ago now so there are some other parameters that are also now available (google should find them for you). Cheers Tom ___

Re: [gmx-users] membrane model

Thanks to all for the useful replies. BTW, which force field will be good option for simulating united-atom (acyl chain) POPC membranes? Many thanks Anu On Fri, Jun 19, 2015 at 5:15 PM, Thomas Piggot wrote: > Good to see the membrane structures have been changed/fixed. I think it > was December

[gmx-users] Free energy calculation

Dear all I'm trying to calculate free energy of solvation according to Justin's tutorial for my protein in water. Is it true to follow that tutorial for my protein? any special changes in MDP file is necessary ? If there is no differences for systems to calculate free energy of solvation accordi

Re: [gmx-users] .xtc and .trr file is missing

Hi RJ, For an XTC file, you need to set nstxtcout (GMX 4.x) or nstxout_compressed (GMX 5). A TPR file is a run _input_ file and is not generated as output. Cheers, Tsjerk On Mon, Jun 22, 2015 at 6:11 AM, RJ wrote: > Dear gmx. > > > I run 100ns simulation of my protein with ligand. After compl