Re: [gmx-users] Making disulfide bonds between protein and glutathion (GSH)

Many thanks Justin :) Tuong Vy 2015-05-28 21:01 GMT+09:00 Justin Lemkul : > > > On 5/27/15 10:23 PM, Vy Phan wrote: > >> Dear Gromas User, >> I want to making disulfide bonds between protein and glutathion (GSH). >> The topology for GSH I got from Produg serve. >> > > Don't do this; the topology

[gmx-users] Should I fix my drugs during membrane penetration simulation?

Dear all, I’m trying to do umbrella sampling simulation which drugs penetrate the POPC membrane. I have trouble what if I do npt or umbrella simulation, the drugs move around from the initial location. (I got each 0.1 nm spacing window for npt and umbrella simulation) So, these results cannot

Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters

I continued to define good partial charges using the tools suggested. I found that the combination of Maestro + ffconv or mktop, ACPYPE and antechamber + mktop have all advantages and disadvantages depending on the organic molecule. for instance for acetone with maestro and mktop i could achiev

Re: [gmx-users] edr file

Not all steps that are attempted actually go down, so the step might get rejected. If the algorithm knew where to go, you wouldn't be running it... Mark On Fri, 29 May 2015 19:43 Andrew Bostick wrote: > Dear Justin, > > Thanks for your answer. > > I know, Energy minimization causes energy to go

[gmx-users] edr file

Dear Justin, Thanks for your answer. I know, Energy minimization causes energy to go down. For example, in following lines, I want to know what value is for step 12 or step 22 in energy minimization? > 11.00 -91587.226562 > 13.00 -93838.976562 or > 21.00 -99023.46093

Re: [gmx-users] edr file

On 5/29/15 1:27 PM, Andrew Bostick wrote: Dear gromacs users After energy minimization, I used g_energy to obtain potential energy vs em steps. g_energy -f em.edr -o potential.xvg. In potential.xvg, some lines are not seen: 0.00 -61742.609375 1.00 -65717.562500 2.00

[gmx-users] edr file

Dear gromacs users After energy minimization, I used g_energy to obtain potential energy vs em steps. g_energy -f em.edr -o potential.xvg. In potential.xvg, some lines are not seen: 0.00 -61742.609375 1.00 -65717.562500 2.00 -75257.804688 3.00 -83263.312500

Re: [gmx-users] Simulation at Different pH's

On 5/29/15 9:05 AM, xy21hb wrote: Dear all, I would like simulate a protein-water binary system at different pH's. The protein is quite typical, could be lysozyme. So no need to worry about proton transfer. Proton transfer can occur for any titratable group; I wouldn't necessarily assume

Re: [gmx-users] rtp file

On 5/29/15 1:08 PM, shahab shariati wrote: Hi all I investigated dna.rtp file in amber03.ff. There is 4 residue types for adenine: DA5, DA, DA3 and DAN. I know about DA5, DA and DA3. But DAN is unknown for me. Please explain about DAN residue type. Isolated nucleotide. Note how it has b

[gmx-users] rtp file

Hi all I investigated dna.rtp file in amber03.ff. There is 4 residue types for adenine: DA5, DA, DA3 and DAN. I know about DA5, DA and DA3. But DAN is unknown for me. Please explain about DAN residue type. Thanks in advance. -- Gromacs Users mailing list * Please search the archive at http:

Re: [gmx-users] check point file

Hi, Please try a quick google search first ;-) Mark On Fri, May 29, 2015 at 6:06 PM Atila Petrosian wrote: > Dear gromacs users > > I have a general question about cpt file. > > Is cpt file created every time mdrun is used, automatically? Or should I > use an special option to create a cpt fil

Re: [gmx-users] User directive for non-bonded interactions

Hi, Yes, back when dinosaurs roamed the earth and the text of that section was first written, it was HTML on the website, and the LaTeX-based manual was available as PDF that people would mostly print. Then someone wrote a script to include the former in the latter, and probably nobody much prints

Re: [gmx-users] User directive for non-bonded interactions

Just to weigh in, I think the unclear part is that the section itself is in the "printed manual" (pdf file). The online manual is copied verbatim into the printed manual as section 7, so statements like that remain. -- James “Wes”​ Barnett Ph.D. Candidate Chemical and Biomolecular Engineering T

[gmx-users] check point file

Dear gromacs users I have a general question about cpt file. Is cpt file created every time mdrun is used, automatically? Or should I use an special option to create a cpt file? For example, if the power fails, how to use the cpt file to resume mdrun? Any help will highly appreciated. -- Groma

[gmx-users] Simulation at Different pH's

Dear all, I would like simulate a protein-water binary system at different pH's. The protein is quite typical, could be lysozyme. So no need to worry about proton transfer. Should I still try constant-pH or any simpler methods available? Thanks, Yao -- Gromacs Users mailing list * Please

Re: [gmx-users] Rule for atom names in GROMACS

On 5/29/15 8:22 AM, Ebert Maximilian wrote: Hi there, While building my own topology I was wondering if the atom name is only used to link .gro atoms with .top entries. The behaviour of an atom is defined by the atom type and the atom name should not have any effect on the simulation right?

[gmx-users] Rule for atom names in GROMACS

Hi there, While building my own topology I was wondering if the atom name is only used to link .gro atoms with .top entries. The behaviour of an atom is defined by the atom type and the atom name should not have any effect on the simulation right? So if I choose an atom name for a carbon as C,

Re: [gmx-users] User directive for non-bonded interactions

Hi Justin, thanks, this does help. The "printed" part confused me, to my mind that's a physical thing, rather than a pdf. Peter On 29/05/15 14:14, Justin Lemkul wrote: > > > On 5/29/15 8:12 AM, Peter Kroon wrote: >> Hi João, >> >> That's where it states "More information is in the printed manual

Re: [gmx-users] PDB files

On 5/29/15 5:38 AM, soumadwip ghosh wrote: Hi all, I have a general query about PDB files. I have made a PDB file for a carbon nanotube (15x15) using VMD which contains 1600 carbon atoms. As far as I know, the PDB file should contain atom no. in lines 13-16 and the residue id in line 18-

Re: [gmx-users] User directive for non-bonded interactions

On 5/29/15 8:12 AM, Peter Kroon wrote: Hi João, That's where it states "More information is in the printed manual". Section 6.10 of the printed manual should cover the details. Is something there unclear? -Justin -- == Justin A. Lemkul,

Re: [gmx-users] User directive for non-bonded interactions

Hi João, That's where it states "More information is in the printed manual". Peter On 29/05/15 14:08, João Martins wrote: > Hi Peter, > > I suppose it refers to the pdf version of the manual, you can find it on > http://www.gromacs.org/Documentation/Manual > > Best regards, > João Martins > > >

Re: [gmx-users] User directive for non-bonded interactions

Hi Peter, I suppose it refers to the pdf version of the manual, you can find it on http://www.gromacs.org/Documentation/Manual Best regards, João Martins *Joao Martins* joaomartins...@gmail.com On Thu, May 28, 2015 at 5:05 PM, Peter Kroon wrote: > Dear list, > > I'm trying to use a tabulat

Re: [gmx-users] [ pairs_nb ] directive problems

Ok, thanks, will do. Cheers, João *Joao Martins* joaomartins...@gmail.com On Fri, May 29, 2015 at 12:14 PM, Mark Abraham wrote: > Hi Joao, > > That's great. You can find my guess at a fixed version, based on the 5.0 > bugfix branch, at https://gerrit.gromacs.org/#/c/4666/. There's a downloa

Re: [gmx-users] [ pairs_nb ] directive problems

Hi Joao, That's great. You can find my guess at a fixed version, based on the 5.0 bugfix branch, at https://gerrit.gromacs.org/#/c/4666/. There's a download link there, where you can get the putative fix in any format that suits you, e.g. various tarballs. You can build and install that in the usu

[gmx-users] PDB files

Hi all, I have a general query about PDB files. I have made a PDB file for a carbon nanotube (15x15) using VMD which contains 1600 carbon atoms. As far as I know, the PDB file should contain atom no. in lines 13-16 and the residue id in line 18-20. Now,I obtained the pdb file from VMD as foll

Re: [gmx-users] [ pairs_nb ] directive problems

Hi Mark, I can do that, where can I find either the fix or the fixed version? João *Joao Martins* joaomartins...@gmail.com On Thu, May 28, 2015 at 4:11 PM, Mark Abraham wrote: > Hi, > > Thanks for the good description of the problem! > > It does look like [ pairs_nb ] is incompletely suppo

Re: [gmx-users] number of Nodes after extension

Thanks Mark! Best regards On Fri, May 29, 2015 at 10:19 AM, Mark Abraham wrote: > Yes you can do that. No, it doesn't matter. > > Mark > > On Fri, May 29, 2015 at 10:16 AM Faezeh Pousaneh > wrote: > > > Hi, > > > > A question please, > > Can I change the number of nodes for the extension of

Re: [gmx-users] number of Nodes after extension

Yes you can do that. No, it doesn't matter. Mark On Fri, May 29, 2015 at 10:16 AM Faezeh Pousaneh wrote: > Hi, > > A question please, > Can I change the number of nodes for the extension of the first run (let us > say first run was with 10 nodes and now I want to increase it to 20 in the > exte

[gmx-users] number of Nodes after extension

Hi, A question please, Can I change the number of nodes for the extension of the first run (let us say first run was with 10 nodes and now I want to increase it to 20 in the extension)? does that influence on the analysis of the runs? thanks. Best regards -- Gromacs Users mailing list * Please