[gmx-users] Which structure to be used during covariance analysis

Hello, I just want to know which structure to be used during covariance analysis with g_covar with -s flag(As stated in manual:All structures are fitted to the structure in the structure file), So which of the following structure would be appropriate to choose for covariance analysis, If we want to

Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

Just curious, this would also hold true for the OPLA-AA force field. It is all-atom, so no changes seems to be necessary besides making a d-amino acid in the input ? On Mon, Mar 28, 2011 at 2:13 PM, Mark Abraham wrote: > On 28/03/2011 8:45 PM, maria goranovic wrote: > > That would mean that a ne

[gmx-users] RE: mathematical expression to obtain the C6 and C12 LJ terms for the GROMOSXX ff family

e OM atom, as an example, why I > > obtained different values for C6 and C12 terms in the [ atomtypes ] > > section. > > > > Thank you again for your help. > > Section 5.3.3 of the manual goes through this. > > Mark >

Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

The best way to find out is by looking at the dihedrals fpor the aminoacid as defined by the forcefield. Someone may know it by heart, but to make sure you need to check it yourself anway. It'll be hard to defend your results before a picky referee by saying that "this dude on a mailing list sa

Re: [gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's

Hi, I've diff-ed the cache file you sent me against the one I generated and I couldn't see anything relevant. Neither does the verbose CMake output suggest anything useful, but that it tries to copy the mdrun-gpu binary from a location where it obviously does not exist. I don't even have this "CMa

Re: [gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's

Hi! tried with cmake 2.8.0 and it seems that is working Thanks for all Szilárd :) Jordi Inglés El 29/03/11 13:00, Szilárd Páll escribió: Hi, I've diff-ed the cache file you sent me against the one I generated and I couldn't see anything relevant. Neither does the verbose CMake output sug

[gmx-users] Atomtype CCL4 not found

Dear users, Force field: 43a1 water model: spc After this command:grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr I have the following error: Fatal error: Atomtype CCL4 not found What should I do? -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gro

Re: [gmx-users] Atomtype CCL4 not found

ahmet yıldırım wrote: Dear users, Force field: 43a1 water model: spc After this command:grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr I have the following error: Fatal error: Atomtype CCL4 not found What should I do? Use an appropriate atom type. The issue is probably capital

Re: [gmx-users] Atomtype CCL4 not found

Dear Justin, There is "CCl4 12.011 ; carbon in carbontetrachloride (solvent)" in the gromos43a1.ff/atomtypes.atp file. But I still have the error "Atomtype CCL4 not found". 2011/3/29 Justin A. Lemkul > > > ahmet yıldırım wrote: > >> Dear users, >> >> Force field: 43a1 >> water model: sp

Re: [gmx-users] Atomtype CCL4 not found

ahmet yıldırım wrote: Dear Justin, There is "CCl4 12.011 ; carbon in carbontetrachloride (solvent)" in the gromos43a1.ff/atomtypes.atp file. But I still have the error "Atomtype CCL4 not found". Exactly as I said, capitalization is your issue. CCl4 and CCL4 are not the same. -J

Re: [gmx-users] Atomtype CCL4 not found

Then, what should I do? 29 Mart 2011 16:36 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> Dear Justin, >> >> >> There is "CCl4 12.011 ; carbon in carbontetrachloride (solvent)" in >> the gromos43a1.ff/atomtypes.atp file. >> But I still have the error "Atomtype CCL4 not

Re: [gmx-users] Atomtype CCL4 not found

ahmet yıldırım wrote: Then, what should I do? You've somehow created a topology that does not conform to the requirements of the force field. Fix it so that it does. -Justin 29 Mart 2011 16:36 tarihinde Justin A. Lemkul > yazdı: ahmet yıldırım wrote:

Re: [gmx-users] Atomtype CCL4 not found

I suppose the term "CCL4" is contained somewhere in the files you use (.top or #included .itp). So dont search in the force field folder but in your working directory. If you found the occurence, replace it with CCl4. For further help it would be better to know the exact error message and/or info

Re: [gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's

Great! I would really appreciate if you could file a bug on redmine.gromacs.org against the build system. Thanks, -- Szilárd On Tue, Mar 29, 2011 at 2:27 PM, Jordi Inglés wrote: > Hi! > > tried with cmake 2.8.0 and it seems that is working > > Thanks for all Szilárd :) > > Jordi Inglés > >

[gmx-users] Re: Which structure to be used during covariance analysis

> Hello, > I just want to know which structure to be used during covariance analysis > with g_covar with > -s flag(As stated in manual:All structures are fitted to the structure in > the structure file), > So which of the following structure would be appropriate to choose for > covariance analysis,

Re: [gmx-users] Atomtype CCL4 not found

Thanks Justin. Problem is solved. .itp file: [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2

[gmx-users] pullx.xvg format

Hi all I have a very quick question. The output for umbrella pulling simulations (pullx.xvg) often appears to have an irregular format, in that the columns don't seem to be perfectly aligned (see below). I have never had a problem with this as g_wham never reported any errors. I was just wondering

Re: [gmx-users] pullx.xvg format

Gavin Melaugh wrote: Hi all I have a very quick question. The output for umbrella pulling simulations (pullx.xvg) often appears to have an irregular format, in that the columns don't seem to be perfectly aligned (see below). I have never had a problem with this as g_wham never reported any err

Re: [gmx-users] Re: Resplica exchange with solute tempering (REST)

On Mon, Mar 28, 2011 at 6:39 PM, Mark Abraham wrote: > On 29/03/2011 4:54 AM, Sai Pooja wrote: > > There was a typo in the mail: > E_protein-protein = Potential - E_water-water - E_protein-water > > On Mon, Mar 28, 2011 at 11:55 AM, Sai Pooja wrote: > >> Hi, >> >> I have tried to implement a va

Re: [gmx-users] pullx.xvg format

Hi Justin Thanks for the reply. I expanded the terminal and it didn't make a difference. Do you still think it's O.K? Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi all >> >> I have a very quick question. The output for umbrella pulling >> simulations (pullx.xvg) often appears

Re: [gmx-users] pullx.xvg format

Gavin Melaugh wrote: Hi Justin Thanks for the reply. I expanded the terminal and it didn't make a difference. Do you still think it's O.K? I don't see why not. If Gromacs produced the output, you didn't change it, g_wham didn't produce an error, and the results weren't completely nonsensi

[gmx-users] Effect of pH on catalytic side

Friends, Need a Gromacs tutorial to find effect of pH on catalytic side. Any help? Regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Plea

Re: [gmx-users] Effect of pH on catalytic side

Monisha Hajra wrote: Friends, Need a Gromacs tutorial to find effect of pH on catalytic side. Any help? There probably isn't one. If it isn't at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, then it doesn't exist. You'll probably want to look into the

Re: [gmx-users] Effect of pH on catalytic side

Monisha Hajra skrev 2011-03-29 17.18: Friends, Need a Gromacs tutorial to find effect of pH on catalytic side. Any help? Regards We're working on the methods and implementation. It'll be a few months until there's a published manuscript. Stay tuned. -- -

Re: [gmx-users] Effect of pH on catalytic side

Thanks Justin. I haven't find any such tutorial or exact relevant research paper. Find some paper though ( http://peds.oxfordjournals.org/content/16/12/1017.full.pdf+html ), not sure how they have done. On Tue, Mar 29, 2011 at 8:51 PM, Justin A. Lemkul wrote: > > > Monisha Hajra wrote: > >> Frie

Re: [gmx-users] Effect of pH on catalytic side

Having only browesd through the papaer very briefly, I can't see how the protonation state was chosen. The modelling part of the paper wasn't that informative. There is a web service called H++ that can make pKa estimates for titrating sites. Not sure how accurate it is though. It uses continuu

Re: [gmx-users] Effect of pH on catalytic side

Thanks Erik for the information. On Tue, Mar 29, 2011 at 9:11 PM, Erik Marklund wrote: > Having only browesd through the papaer very briefly, I can't see how the > protonation state was chosen. The modelling part of the paper wasn't that > informative. There is a web service called H++ that can

[gmx-users] Re: g_cluster segmentation fault

Hi Mark, Works perfectly... Thanks, Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK On 26/03/11, Craig Kitchen wrote: Dear All, When running g_cluster on a file generated with g_mdmat I receive a segmentation fault. I have tried dif

[gmx-users] g_gyrate options

Hi everyone, I have a question about -nmol option of g_gyrate -h : With the -nmol option the radius of gyration will be calculated for multiple molecules by splitting the analysis group in equally sized parts. If there are 4 chains ABCD in the solvent, and each chain has n atoms of different typ

Re: [gmx-users] Re: Which structure to be used during covariance analysis

Hi Bipin, That won't really matter. The reference is just for fitting. Cheers, Tsjerk On Mar 29, 2011 3:51 PM, "bipin singh" wrote: > > Hello, > I just want to know which structure to be used during covariance analysis with g_cov... -- gmx-users mailing listgmx-users@gromacs.org http://l

Re: [gmx-users] Re: Which structure to be used during covariance analysis

Thanks Sir for you help regarding the doubt On Tue, Mar 29, 2011 at 22:49, Tsjerk Wassenaar wrote: > Hi Bipin, > > That won't really matter. The reference is just for fitting. > > Cheers, > > Tsjerk > > On Mar 29, 2011 3:51 PM, "bipin singh" wrote: > > > > Hello, > I just want to know w

Re: [gmx-users] Re: Resplica exchange with solute tempering (REST)

It is working. The error was clerical. Thank you for your time. On Tue, Mar 29, 2011 at 10:52 AM, Sai Pooja wrote: > > > On Mon, Mar 28, 2011 at 6:39 PM, Mark Abraham wrote: > >> On 29/03/2011 4:54 AM, Sai Pooja wrote: >> >> There was a typo in the mail: >> E_protein-protein = Potential - E_wat

Re: [gmx-users] Placing ions at a required distance

Thanks, I did it manually using 'cat'. Thanks for your time. -Shivangi On Mon, Mar 28, 2011 at 4:47 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hi again, >> >> I did not quite understand the suggestion. >> I have successfully added Li+ ions in my simulation box using genion. >

[gmx-users] Check for bad contacts and/or reduce the timestep.

Hello gmx-users, I have a 5 ang box with equal number of water and methanol molecules (1800), a neutral peptide, 8 hydroxide ions and 10 Li+ ions. The system is overall +2 charged. I am trying to to do a NVT equilibration which runs into the following error: t = 0.000 ps: Water molecule startin

Re: [gmx-users] Check for bad contacts and/or reduce the timestep.

shivangi nangia wrote: Hello gmx-users, I have a 5 ang box with equal number of water and methanol molecules (1800), a neutral peptide, 8 hydroxide ions and 10 Li+ ions. The system is overall +2 charged. If your box truly is 5 A (0.5 nm), grompp should have failed based on your cutoffs.

Re: [gmx-users] oligoglycines

Thanks Tsjerk! Looks like it is working! Quoting Tsjerk Wassenaar : Hi Nisha, For building you can also use pymol if you have it installed. On the command line you can issue: pymol -qcd 'editor.build_peptide("GGG");cmd.save("triglycine.pdb","not hydro")' Hope it helps, Tsjerk On Mon,

[gmx-users] Alternating electric fields in GROMACS

Dear all, I wonder if the alternating electric fields are implemented in the newly released GROMACS or somewhere, mayebe in the cvs code. If not, could someone give me a tip on how to do such revisions. Any suggestions are appreciated! As far as I know, it seems for a really long time that the man

Re: [gmx-users] Check for bad contacts and/or reduce the timestep.

Hello, I am sorry, I did mean 5 nm box. I did do the energy minimization but somehow overlooked the error message at that stage. Things seems to be working now. Thanks for the time. Shivangi On Tue, Mar 29, 2011 at 2:06 PM, Justin A. Lemkul wrote: > > > shivangi nangia wrote: > >> Hello gmx

[gmx-users] Error in GROMACS installation

Hi All, I am installing GROMACS using cygwin. I am following the steps as mentioned : http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO *no 5, make install command give the following error in the end :* ng' Creating library file: .libs/libgmx.dll.a collect2: ld returned 1

Re: [gmx-users] Error in GROMACS installation

Monisha Hajra wrote: Hi All, I am installing GROMACS using cygwin. I am following the steps as mentioned : http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO *no 5, make install command give the following error in the end :* What was your configuration command? Did "

[gmx-users] SO4

Hi, I posted this question about SO42- in GROMACS two months ago, but I would like to double-check to confirm my MD results: 1. I used gromos53a6.ff force forced for SO42- ion. I have 4 "SO4" ions in the original pdb file. 2. When I changed the name "SO4" to "SO42-" in the pdb file as shown in th

Re: [gmx-users] SO4

simon sham wrote: Hi, I posted this question about SO42- in GROMACS two months ago, but I would like to double-check to confirm my MD results: 1. I used gromos53a6.ff force forced for SO42- ion. I have 4 "SO4" ions in the original pdb file. 2. When I changed the name "SO4" to "SO42-" in the p

Re: [gmx-users] Alternating electric fields in GROMACS

On 2011-03-29 20.42, Bert wrote: Dear all, I wonder if the alternating electric fields are implemented in the newly released GROMACS or somewhere, mayebe in the cvs code. If not, could someone give me a tip on how to do such revisions. Any suggestions are appreciated! As far as I know, it seems

[gmx-users] Strange behavior from g_sas

Hi, all, I have four trajectories which I want to analyze Surface on. So I run for i in 1 2 3 4; do echo -e " non-Water \n Protein " | g_sas -f $i.xtc -s $i.tpr -o $i.area.xvg -n index.ndx -q $i.pdb ; done But the strange thing is, g_sas analyzed the first three trajectories, but gave a "seg