Re: [gmx-users] adding new ion within the oplsaa force field

yes, the ions I have can be considered as bound. I found out I also had to declare the type of residue as "Ion" in file residues.dat :) On Fri, Jun 23, 2017 at 4:44 PM, Justin Lemkul wrote: > > > On 6/23/17 3:50 PM, Jose Borreguero wrote: > >> Dear Gromacs users, >> >> I'm

Re: [gmx-users] adding new ion within the oplsaa force field

On 6/23/17 3:50 PM, Jose Borreguero wrote: Dear Gromacs users, I'm trying to add a new type of atom as an ion. Looking at already existing ions, such as sodium (NA), I see there's an entry both in files ions.itp and aminoacids.rtp. My question is, what is the rationale of declaring ions both

Re: [gmx-users] adding new ion within the oplsaa force field

If you want the ion to be recognized as an individual residue, you need to stick it in the *.rtp file. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics

[gmx-users] adding new ion within the oplsaa force field

Dear Gromacs users, I'm trying to add a new type of atom as an ion. Looking at already existing ions, such as sodium (NA), I see there's an entry both in files ions.itp and aminoacids.rtp. My question is, what is the rationale of declaring ions both as ions and as residues? Is this always

Re: [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

Dear sir i have force field for O2 now some one work over it before its the .prm file he use to run simulation amber99 force field and use there own lab heme generated ff heme fe 02 now how i can use these amber heme force field in Gromacs thanks. On Fri, Jun 16, 2017 at 3:23 AM, Mark

Re: [gmx-users] Scaling GROMACS

Hi, Once you've compiled GROMACS for this machine (will run at least twice as fast), your setup is likely optimal. The options and what to do with them are all in the 5.1 gromacs user guide online. Mark On Fri, 23 Jun 2017 16:10 Sergio Manzetti wrote: > Hi, I

Re: [gmx-users] CGMD with cut-off Verlet?

Hi, And follow the advice of the Martini authors for using the Verlet scheme with their forcefield. Mark On Fri, 23 Jun 2017 17:20 Justin Lemkul wrote: > > > On 6/23/17 11:08 AM, Alex Mathew wrote: > > Dear all, > > > > While running CGMD in GPU i got this error > > > >

Re: [gmx-users] Constraint vs. Umbrella in Pull COM

Thank you for the clarification! -Angela From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Alex Sent: June 22, 2017 7:57 PM To: Discussion list for GROMACS users

Re: [gmx-users] Scaling GROMACS

On 6/23/17 10:04 AM, Sergio Manzetti wrote: Hi, I have the following system: Running on 1 node with total 24 cores, 24 logical cores Hardware detected: CPU info: Vendor: AuthenticAMD Brand: AMD Opteron(tm) Processor 6344 SIMD instructions most likely to fit this hardware: AVX_128_FMA SIMD

Re: [gmx-users] CG MD

On 6/23/17 10:26 AM, Alex Mathew wrote: Dear all, I was wondering the analysis we usually use in the all-atom simulation will work in for CG model? I guess secondary structural analysis will be useless since it's not considering all atoms. What about non-bonded energies and other parameters

Re: [gmx-users] CGMD with cut-off Verlet?

On 6/23/17 11:08 AM, Alex Mathew wrote: Dear all, While running CGMD in GPU i got this error OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet Here can i change the cut-off scheme to Verlet ? Amazingly enough:

[gmx-users] Exchange temperature instead of exchange coordinate in replica exchange molecular dynamics?

Hi all, I am reading the paper "Replica-exchange molecular dynamics method for protein folding" by Yuko Okamoto. In this paper, they exchange temperatures of 2 replica. To evaluate that replica exchange is successful, they calculate exchange probability; plot the temperature, potential energy per

[gmx-users] CGMD with cut-off Verlet?

Dear all, While running CGMD in GPU i got this error OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet Here can i change the cut-off scheme to Verlet ? ff is martini22p -- Gromacs Users mailing list * Please search the

[gmx-users] Legacy Test Failure with GMX 5.1.4

Hello, I am recompiling GROMACS on a new compute node and I am getting a unit test failure (shown below). I am compiling with GNU 4.8.5 and the following cmake commands: cmake .. -DCMAKE_INSTALL_PREFIX=[redacted] -DGMX_MPI=on -DGMX_GPU=off -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

[gmx-users] CG MD

Dear all, I was wondering the analysis we usually use in the all-atom simulation will work in for CG model? I guess secondary structural analysis will be useless since it's not considering all atoms. What about non-bonded energies and other parameters such hydrogen bond and essential dynamics?

[gmx-users] Scaling GROMACS

Hi, I have the following system: Running on 1 node with total 24 cores, 24 logical cores Hardware detected: CPU info: Vendor: AuthenticAMD Brand: AMD Opteron(tm) Processor 6344 SIMD instructions most likely to fit this hardware: AVX_128_FMA SIMD instructions selected at GROMACS compile

Re: [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

The problem has been solved. I forgot to delete some entries when using .top file as .itp file. Thanks, Qing At 2017-06-23 15:36:32, "Mark Abraham" wrote: >Hi, > >You can't just paste together two topology files intended to stand alone >e.g. because they have

Re: [gmx-users] 5-letter atom names in topology files

At 2017-06-23 21:55:39, "Justin Lemkul" wrote: > > >On 6/23/17 9:53 AM, Qing Lv wrote: >> I tried pdb2gmx -merge interactive or -chainsep interactive, but neither >> work... > >There is no chain information in a .gro so this approach cannot work. If you >have a multimeric

Re: [gmx-users] 5-letter atom names in topology files

On 6/23/17 9:53 AM, Qing Lv wrote: I tried pdb2gmx -merge interactive or -chainsep interactive, but neither work... There is no chain information in a .gro so this approach cannot work. If you have a multimeric complex, and you need to use these weird 5-character names, process each .gro

Re: [gmx-users] 5-letter atom names in topology files

I tried pdb2gmx -merge interactive or -chainsep interactive, but neither work... Qing At 2017-06-23 17:19:55, "Fitsiou, Eleni" wrote: >Hi , >Rename your chains and you could use -merge interactive and the -ter flag >Best >-- >Gromacs Users mailing list > >*

Re: [gmx-users] Gigantic boxes

Thanks, that fixed it! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [

Re: [gmx-users] Regarding creating a itp for molecule from CGenFF

On 6/23/17 1:02 AM, Dilip H N wrote: Hello all, I want to simulate methylamine with amino acid misture in CHARMM FF, so i have created methylamine in mol2 format and created the .itp and .pdb files from the CGenFF (which creates itp in CHARMM FF for GROMACS). and i have included it in

Re: [gmx-users] Gigantic boxes

On 6/23/17 6:20 AM, Sergio Manzetti wrote: Hi, I Have prepared a box, which just grows beyond proportions in order to satisfy grompp complaining about the box being less than the double of rlist, so decrease rlist or increase the box. As rlist has to be 8 for AMBER, the box quickly becomes

[gmx-users] Box size and Force field

Hi, it seems that there is something with the force field that gives issues: The same parameters are used for 5 molecules in a test run: Using AMBER99SB ISTN : 2 of 5 small molecules work perfectly in the simulation in water. 3 of the 5 small molecules stop at grompp MD.mdp step giving the

[gmx-users] Gigantic boxes

Hi, I Have prepared a box, which just grows beyond proportions in order to satisfy grompp complaining about the box being less than the double of rlist, so decrease rlist or increase the box. As rlist has to be 8 for AMBER, the box quickly becomes over 14x14x14. When one visualizes it one can

Re: [gmx-users] 5-letter atom names in topology files

Hi , Rename your chains and you could use -merge interactive and the -ter flag Best -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists *

Re: [gmx-users] 5-letter atom names in topology files

My protein contains 2 chains, and ILE294 is the C-terminus of chain 1. When I used pdb2gmx to process the GRO file, it can recognize N-terminus of chain 1 and C-terminus of chain 2, but cannot recognize C-terminus of chain 1. Since there is no chain separators in GRO files (like "TER" in PDB),

Re: [gmx-users] 5-letter atom names in topology files

Dear Mark, Actually I had tried the method you suggested, but got such errors (pdb2gmx): Fatal error: Atom O1 in residue ILE 294 was not found in rtp entry ILE with 9 atoms while sorting atoms. ILE294 is C-terminus of my protein. I looked up in aminoacids.rtp and there are no atom "O1" or "O2"

Re: [gmx-users] Pulling inside a channel to calculate the PMF

Thanks Alex, finding the positions as you propose seems a legitimate way for this problem. One will have to wait enough with a classical MD but Bias MD should help. In my case the channel is not a large ion channel. FR. 2017-06-22 18:26 GMT+02:00 Alex : > I've never used

Re: [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

Hi, You can't just paste together two topology files intended to stand alone e.g. because they have [defaults] sections. You can #include files, but they have to follow the structure of the example in chapter 5 of the manual (and every tutorial). Defaults, then atomtypes and parameters, then

Re: [gmx-users] 5-letter atom names in topology files

Hi, I suggest you produce your initial conformation in .gro format, which permits five-character atom names. That might mean using editconf on your .pdb file, and then manually renaming atoms. Mark On Fri, Jun 23, 2017 at 3:55 AM Qing Lv wrote: > Hi, > > > Gromos 54a7