[gmx-users] gmx sasa output group not recognised

Good morning, I've recently started using gromacs 5.0.4 and I can't make"gmx sasa" to recognise non-standard groups for the -output flag. I have three groups (G6P, Co-enzyme and strNADP+; all subset of the dimer ) and every time I specify one of the three with "-output" flag I get: "Inconsistency

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

Matthew, Quick question, what are you trying to examine with the addition of bicarbonate? -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics

Re: [gmx-users] gmx sasa output group not recognised

Hello, On Fri, Sep 4, 2015 at 1:51 PM Francesco Carbone wrote: > I've recently started using gromacs 5.0.4 and I can't make"gmx sasa" to > recognise non-standard groups for the -output flag. > I have three groups (G6P, Co-enzyme and strNADP+; all subset of the dimer ) >

Re: [gmx-users] gmx sasa output group not recognised

The other possibility is that your index groups do not have the atom indices in an increasing order. If this is the case, just sort the atoms, or don't use make_ndx as an intermediate step. Teemu On Fri, Sep 4, 2015, 14:20 Francesco Carbone wrote: > thank you for the

Re: [gmx-users] mdp file

Thanks for your quick reply. Up till now all the simulations I have performed are with the OPLS force field, because the software I used in the past supported only that in the academic version. Anyway, to sum it up for non bonded from the literature about a particular force field and try some

Re: [gmx-users] Input files for performance analysis

Hi, > On 03 Sep 2015, at 13:07, Sabyasachi Sahoo wrote: > > Thank you for the papers, but can I get access to zipped files containing > input files( like .mdp and .topol or even .tpr file) that can be directly > simulated. You will find them in the ’supplements’ box on

Re: [gmx-users] CMAP missing for a new residue.

It seems to work :). Thank you! 2015-09-04 9:52 GMT+01:00 Dawid das : > > 2015-09-03 13:06 GMT+01:00 Justin Lemkul : > >> FYI, CHARMM22 has no CMAP. CHARMM22/CMAP (what GROMACS somewhat >> misleadingly calls "charmm27.ff") does. >> > Yes, I was aware of

Re: [gmx-users] Input files for performance analysis

Thanks a lot Carsten. I am really grateful for this material. On Fri, Sep 4, 2015 at 3:04 PM, Kutzner, Carsten wrote: > Hi, > > > On 03 Sep 2015, at 13:07, Sabyasachi Sahoo > wrote: > > > > Thank you for the papers, but can I get access to zipped files

Re: [gmx-users] gmx sasa output group not recognised

thank you for the reply, but the residues are in the same protein. I simply select a list of residues that interact with the substrate. (echo "r 171 263 201 202 205 395 365 239 360 258"; echo "name 10 G6P"; echo "q") | make_ndx -f $nameprod.gro -o $name1.ndx residues 171 263 201 202 205 395 365

[gmx-users] problem with gpu performance

Dear Gromacs Users I am trying to run gpu version of gromacs5.0.6 in a work-station which is a hexacore processor that can be multithreaded to 12. The workstation has 2 Geforce GT 610 GPUs . I am finding the simulation using -nb gpu is exceedingly slower than -nb cpu ( i,e turning off gpu) I

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

On 9/4/15 9:07 AM, Faulkner, Matthew wrote: Thank you Justin, Do you know a suitable force field to use for a topolgy from PRODRG? I am aware that the topology from PRODRG may now be of the best quality but I want to run a short MDS as proof of concept first to see if the events I am

[gmx-users] Entropy calculations for simple systems (water)

Dear all, I'm trying to perform entropy calculations with GROMACS. To get started I'm trying to get the entropy of water using the TIP4P and TIP3P models. At the moment I'm running a MD simulation of different size boxes for around 1ns and using the following analysis tools: g_covar_d -f

Re: [gmx-users] problem with gpu performance

On 9/4/15 10:35 AM, Peter Kroon wrote: Hi Jagannath, I don't dare comment on these specifics. There's probably some (gromacs specific) benchmarks out there *somewhere*, quite possibly on this list. But maybe someone else on the list knows what you should get :) Quoting Carsten from a few

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

On 9/4/15 7:42 AM, Faulkner, Matthew wrote: I am trying to find a suitable force field for using Bicarbonate in an aqueous environment in my MDS. I can't find anything where Bicarbonate has been used this way in gromacs in the literature, does anybody know of a reference for me or have advice

Re: [gmx-users] problem with gpu performance

Hi Peter Thanks for your response. I also realized that GTX-610 is not able to catch up with the faster cpu ( Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz). I tried cpu-gpu combination for -nb option. It improves it slightly but not by much. So, we are planning to go for a replacement of GPU cards.

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

Thank you Justin, I will check the charges. I appreciate the help. Matthew. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 04 September

Re: [gmx-users] problem with gpu performance

Hi Jagannath, I don't dare comment on these specifics. There's probably some (gromacs specific) benchmarks out there *somewhere*, quite possibly on this list. But maybe someone else on the list knows what you should get :) Peter On 04/09/15 15:58, jagannath mondal wrote: > Hi Peter > Thanks

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

Micholas, I have a protein which has a pore through the centre believed to act as channel for a range of molecules, Bicarbonate is one of them. I want to see if Bicarbonate passes through the channel and what happens as it does. I already have interesting events like this for ions I can add

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

Thank you Justin, Do you know a suitable force field to use for a topolgy from PRODRG? I am aware that the topology from PRODRG may now be of the best quality but I want to run a short MDS as proof of concept first to see if the events I am interested in occur in a reasonable timeframe.

Re: [gmx-users] problem with gpu performance

-Original Message- From: "jagannath mondal" Sent: ‎9/‎4/‎2015 6:32 PM To: "gromacs.org_gmx-users@maillist.sys.kth.se" Subject: [gmx-users] problem with gpu performance Dear Gromacs Users I am trying to run gpu version

Re: [gmx-users] problem with gpu performance

Hi Jagannath, AFAIK GT610's are rather slow. What you could try is using both cpu and gpu for non-bonded interactions (-nb gpu_cpu) Peter On 04/09/15 15:01, jagannath mondal wrote: > Dear Gromacs Users > > I am trying to run gpu version of gromacs5.0.6 in a work-station which is > a hexacore

Re: [gmx-users] Entropy calculations for simple systems (water)

Dear Miguel, it appears that the water dynamics is far from being harmonic thus the analysis of the covariance matrix would be useless. You may wish to check the following paper: Reinhard F, Grubmüller H. Estimation of absolute solvent and solvation shell entropies via permutation reduction. J.

Re: [gmx-users] Carbohydrate GAG simulations

Dear Neha ! Thank you for the reply .I am happy that you gave all possible ways to do it . It will be definitely helpful for a beginner like me. On Thu, Sep 3, 2015 at 11:36 PM, Neha Gandhi wrote: > Hi Lara, > > I have worked extensively on GAGS in particular heparin.

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

My group works with the bicarbonate and similar anions in the context of CO2 chemisorption. You must exercise serious caution to assign correct electrostatic potential at the surface of the anion and account for hydration/solvation effects within the force field derivation procedure. On Fri,

[gmx-users] Heating step by step.

Dear Gromacs Experts, Is it possible to do following heating of my system: increase reference temperature by 20 K every 5 ps of simulation in one run until I reach 300 K? According to what I found in one of papers, it is possible to do with NAMD. Best wishes, Dawid Grabarek -- Gromacs Users

Re: [gmx-users] Invalid order for directive atomtypes-

Dear Justin, Thanks for you quick answer, I checked the your suggested link. these new types and their associated parameters must appear before any [moleculetype] directive. In my lig.itp file, [ atomtypes ] appeared before [ moleculetype ] directive. [ atomtypes ] ;name bond_typemass

Re: [gmx-users] Invalid order for directive atomtypes-

On 9/4/15 2:51 PM, Atila Petrosian wrote: Dear Justin, I confused. In your tutorial (protein-ligand) ( http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html), you used the following lines (in my case, I did like you) ; Include Position restraint file

Re: [gmx-users] Heating step by step.

On 9/4/15 1:04 PM, Dawid das wrote: Dear Gromacs Experts, Is it possible to do following heating of my system: increase reference temperature by 20 K every 5 ps of simulation in one run until I reach 300 K? http://manual.gromacs.org/online/mdp_opt.html#sa -Justin --

Re: [gmx-users] Invalid order for directive atomtypes-

On 9/4/15 2:30 PM, Atila Petrosian wrote: Dear Justin, Thanks for you quick answer, I checked the your suggested link. these new types and their associated parameters must appear before any [moleculetype] directive. In my lig.itp file, [ atomtypes ] appeared before [ moleculetype ]

[gmx-users] Invalid order for directive atomtypes-

Dear gromacs users, My system contains protein and ligand. I get conf.gro and topol.top for protein using pdb2gmx. I used antechamber and acpype for my ligand. I get 2 files: lig.top and lig.gro. Since it should be just 1 topology file, I modified lig.top as lig.itp and included it in topolo.top

Re: [gmx-users] Invalid order for directive atomtypes-

Dear Justin, I confused. In your tutorial (protein-ligand) ( http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html), you used the following lines (in my case, I did like you) ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif *;

Re: [gmx-users] When is it necessary to use the -nopbc option in GROMACS analysis tools (i.e. g_sas)?

Only if you do fitting. Cheers, Tsjerk On Thu, Sep 3, 2015 at 2:08 PM, Justin Lemkul wrote: > > > On 9/3/15 5:23 AM, Bernhard Reuter wrote: > >> Dear all, >> >> Is it necessary to use the -nopbc option ("By default, periodic boundary >> conditions are taken into account, this

Re: [gmx-users] Heating step by step.

annealing-time: 0.000 0.001 5.000 5.001 10.000 10.001 15.000 annealing-temp: 0 20 20 40 40 60 60 However, your simulation schedule makes little sense physically . Remember that what you change here of the thermostat's reference temperature,

[gmx-users] bonds, angles, and dihedrals in .rtp file format

Dear Gromacs users, I want to know if it is mandatory to add bonds, angles, and dihedrals in the .rtp file for a novel residue? According to Gromacs manual you need to add atoms and charges, only. Truly yours, Farideh -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Invalid order for directive atomtypes-

On 9/4/15 1:57 PM, Atila Petrosian wrote: Dear gromacs users, My system contains protein and ligand. I get conf.gro and topol.top for protein using pdb2gmx. I used antechamber and acpype for my ligand. I get 2 files: lig.top and lig.gro. Since it should be just 1 topology file, I modified

Re: [gmx-users] Heating step by step.

2015-09-04 22:03 GMT+01:00 Vitaly V. Chaban : > However, your simulation schedule makes little sense physically . > What do you mean by that? I just want to heat up my system gently before equilibration phase. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Error while using grompp

Yes, I tried using Verlet cutoff scheme but, its giving me error that cut-off is smaller than half box vector, which implies that I am making some error in the simulation (though I followed everything given on that tutorial) or probably few tweaks in the .mdp or some file might help. I will be

Re: [gmx-users] CMAP missing for a new residue.

2015-09-03 13:06 GMT+01:00 Justin Lemkul : > FYI, CHARMM22 has no CMAP. CHARMM22/CMAP (what GROMACS somewhat > misleadingly calls "charmm27.ff") does. > Yes, I was aware of that, just forgot to write CHARM22/CMAP. > > My question is, whether there is a way to use CMAP