[gmx-users] Topology file for Fullerene with OPLS_AA force field

Hi Gromacs users ,  I want to have a system with one C60 and about 1000 water molecules .I tried to use pdb2gmx on C60.pdb but I got fatal error , I think the problem is because of my PDB file .I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use

[gmx-users] Pi stacking

Hi all, I want to ask a very general question which was asked by one of the reviewer of my paper. I have shown the stacking between different base pairs of a single stranded DNA at different salt concentration. The corresponding distances between the stacked base pairs were estimated using

Re: [gmx-users] A simple question

Can you please let me know what the problem is ?  From: saeed poorasad To: "Smith, Micholas D." ; "gmx-us...@gromacs.org" Sent: Tuesday, 14 April 2015, 9:59 Subject: Re: [gmx-users] A simple question Dear Dr.Smith , Thanks for your replay . This is a part of my PDB file :  ATOM    

[gmx-users] Fe2+ non bonded parameters for AMBER

Dear Users, Had anybody used Fe2+ ions in the active site of protein. I am planning to use one using amber99sb forcefield...please suggest to use the nonbonded parameters for Fe2+ ions, sigma and epsilon values. Kind regards, Raja -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] there wasn't md_0_1.xtc file

Hi every body I have two questions? 1- accroding to the previos email, I used gromacs to run a covalent bond, for the first try,I run my covalent bond based on the tutorail (lysozyme in water) that nstxtcout = 0 was in md.mdp file, so I changed nstxtcout =0 to >0 and run was repeated. in the both

Re: [gmx-users] Fatal error: Atom type Zn2+ (residue ZN) not found in atomtype database

I guess , the force filed you are using doesn't have ZN atom defined in atomtypes , you can define it manually or use other forcefileds which has it defined already On Thu, Apr 9, 2015 at 9:23 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Dear all > > I am running pdb2gmx to cre

Re: [gmx-users] adding SR2++ to charm27 force field

Dear Justin and mark, I modified the files like this: aminoacids.rtp [ MG ] [ atoms ] MG MG 2.000 [ SR ] [ atoms ] SR SR 2.000 ions.itp [ moleculetype ] ; molname nrexcl MG 1 [ atoms ] ; idat type res nr residu name at name cg

Re: [gmx-users] problem with dihedral restraints in gromacs 5.0.4

> > > On 4/10/15 12:06 PM, Agnieszka Slowicka wrote: >> Hello, >> I have a problem with implementation of dihedral restraints in gromacs 5.0.4. >> I introduced restraints into a topology file after the section with protein topology as fallowing: >> ; dihedral restraints added manually: phi,psi, chi

Re: [gmx-users] How to get the .gro file for MgO surface

You probably mean the topology, which you will have to build yourself, likely at the forcefield level. Is there any particular reason for trying to simulate metal oxide with GMX? There are much better tools suited for this, e.g. LAMMPS with ReaxFF. Alex z> Dear you, z> Does any

Re: [gmx-users] How to get the .gro file for MgO surface

On 4/14/15 10:10 PM, zhp1006 wrote: Dear you, Does anyone know how to get the .gro file for MgO surface? The pdb2gmx and Prodrg could not do that. Both of those are tools primarily for building topologies. If you have coordinates in a different format and want to conv

[gmx-users] How to get the .gro file for MgO surface

Dear you, Does anyone know how to get the .gro file for MgO surface? The pdb2gmx and Prodrg could not do that. Best regards Hongping -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before pos

Re: [gmx-users] R-B dihedrals

Mark, we just figured it out, thanks. :) And yes, you are definitely onto something: two identical dihedrals pulling in opposite directions. This is what happens when people from solid state show up to use GMX. :) Alex On Tue, Apr 14, 2015 at 5:20 PM, Mark Abraham wrote: > Can you shift it to 4

Re: [gmx-users] R-B dihedrals

Can you shift it to 40 degrees? Mark On Tue, Apr 14, 2015 at 11:26 PM, Alex wrote: > Absolutely nothing in between, this is (cos(45)-cos(phi))^2, two minima at > 45 and 315 and a peak around 180. Checked if I converted to R-B > coefficients correctly -- same thing. At 90/270 clean decrease to 4

Re: [gmx-users] How to call an external LAPACK function in gromacs

Hi, I just found that changing from "dpotrf" to "dpotrf_" in the source code would solve the problem... sorry for the trouble. Sincerely, Qian On Tue, Apr 14, 2015 at 3:11 PM, qian wang wrote: > Hi, > > *>> Please try the latest 5.0.4 release, we might well have fixed a bug in > the template c

Re: [gmx-users] R-B dihedrals

Absolutely nothing in between, this is (cos(45)-cos(phi))^2, two minima at 45 and 315 and a peak around 180. Checked if I converted to R-B coefficients correctly -- same thing. At 90/270 clean decrease to 45/315. Alex On Tue, Apr 14, 2015 at 3:16 PM, Justin Lemkul wrote: > > > On 4/14/15 5:12

Re: [gmx-users] R-B dihedrals

On 4/14/15 5:12 PM, Alex wrote: Tried both, the (now enormous) parameters are read in correctly, nothing in output mdp that catches my eye. No constraints used in the system, explicitly set in mdp. Plotted the potential at 45/315 deg minimum -- definitely nonzero at 90 degrees (starting config)

Re: [gmx-users] R-B dihedrals

Tried both, the (now enormous) parameters are read in correctly, nothing in output mdp that catches my eye. No constraints used in the system, explicitly set in mdp. Plotted the potential at 45/315 deg minimum -- definitely nonzero at 90 degrees (starting config). This has got to be the strangest G

Re: [gmx-users] Position restraint for ions

On 4/14/15 4:50 PM, Marcelo Depólo wrote: 2015-04-14 17:26 GMT-03:00 Justin Lemkul On 4/14/15 3:25 PM, Marcelo Depólo wrote: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topolo

Re: [gmx-users] Position restraint for ions

2015-04-14 17:26 GMT-03:00 Justin Lemkul > > > On 4/14/15 3:25 PM, Marcelo Depólo wrote: > >> *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in >>> position_restraints out of bounds (1-1748).This probably means that you > have inserted topology section "position_restrain

Re: [gmx-users] R-B dihedrals

Hi Alex, Maybe writing out the preprocessed topology (grompp -pp) or checking the .tpr with gmxdump can show whether the dihedral parameters are really what you think they are. Cheers, Tsjerk On Apr 14, 2015 10:32 PM, "Alex" wrote: > I have a set of dihedrals described by the R-B potential, wi

[gmx-users] R-B dihedrals

I have a set of dihedrals described by the R-B potential, with a minimum at 90 degrees, and minimization indeed yielded angles very close to that. At some point, I decided to check if I can rotate the groups to another angle, say, 45 degrees. Simple enough, so I changed the expression. Energy mini

Re: [gmx-users] Position restraint for ions

On 4/14/15 3:25 PM, Marcelo Depólo wrote: *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in position_restraints out of bounds (1-1748).This probably means that you have inserted topology section "position_restraints"in a part belonging to a different molecule than you intended

Re: [gmx-users] How to call an external LAPACK function in gromacs

Hi, *>> Please try the latest 5.0.4 release, we might well have fixed a bug in the template compilation stuff.* I just tried 5.0.4 and have the same error. *>> Even then, per the README you will find in share/template, you will might have to teach CMake that it should augment the linking path.

Re: [gmx-users] Position restraint for ions

> *Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in >>> position_restraints out of bounds (1-1748).This probably means that you >>> have inserted topology section "position_restraints"in a part belonging >>> to >>> a different molecule than you intended to.In that case move the >>>

Re: [gmx-users] Position restraint for ions

2015-04-14 14:54 GMT-03:00 Justin Lemkul : > > > On 4/14/15 1:48 PM, Marcelo Depólo wrote: > >> Hi! >> >> >> I was wondering if there is any clear way to create position restraints >> for >> ions. I am using: >> >> *g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group >> "non-Water

Re: [gmx-users] Position restraint for ions

On 4/14/15 1:48 PM, Marcelo Depólo wrote: Hi! I was wondering if there is any clear way to create position restraints for ions. I am using: *g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group "non-Water"'* -> to create an index for my RNA and Ions; and: *genrestr -f rna_i

[gmx-users] Position restraint for ions

Hi! I was wondering if there is any clear way to create position restraints for ions. I am using: *g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group "non-Water"'* -> to create an index for my RNA and Ions; and: *genrestr -f rna_ions.gro -n rna_ion.ndx -o rna_ion.itp -fc 800

Re: [gmx-users] How to call an external LAPACK function in gromacs

Hi, On Tue, Apr 14, 2015 at 4:15 PM, qian wang wrote: > Hi, > > Here is the information. Thank you. > > cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on > -DCMAKE_PREFIX_PATH=/usr/lib64: > > Looking for sgemm_ > -- Looking for sgemm_ - found > -- A library with BLAS API found. > --

Re: [gmx-users] adding SR2++ to charm27 force field

On Tue, Apr 14, 2015 at 11:12 AM, Ming Tang wrote: > Hi Mark, > > Thanks for your reply. I am sure as I changed the files in the charmm27.ff > installed in my unbuntu system. Is there any other things I need to > consider? > pdb2gmx lists the full path to the folder in which it finds the files i

Re: [gmx-users] adding SR2++ to charm27 force field

On 4/14/15 5:12 AM, Ming Tang wrote: Hi Mark, Thanks for your reply. I am sure as I changed the files in the charmm27.ff installed in my unbuntu system. Is there any other things I need to consider? The files you listed are the only ones that should need to be modified. Either you missed

Re: [gmx-users] How to add a repulsive harmonic potential

On 4/14/15 3:13 AM, atsutoshi.ok...@takeda.com wrote: Depending on how structurally complex the ligands are, it may be very easy to define a dummy atom within the structure using a virtual site, then specifying a nonbonded interaction only between these virtual sites using [nonbond_params]. Tha

Re: [gmx-users] How to call an external LAPACK function in gromacs

Hi, Here is the information. Thank you. cmake .. -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DCMAKE_PREFIX_PATH=/usr/lib64: Looking for sgemm_ -- Looking for sgemm_ - found -- A library with BLAS API found. -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK AP

Re: [gmx-users] Clusters

On Tue, Apr 14, 2015 at 2:45 AM, Lucas Dadalt Morero wrote: > Sorry, it's 8 cores. Network is good. Good for what? I was hoping to hear that it's e.g IB QDR. Otherwise it's unlikely that you'll scale to all nodes. > The hardware setup is ok, I just want to know how to perform a gromacs > simula

Re: [gmx-users] adding SR2++ to charm27 force field

Hi Mark, Thanks for your reply. I am sure as I changed the files in the charmm27.ff installed in my unbuntu system. Is there any other things I need to consider? Thanks, Ming -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun

Re: [gmx-users] Print Charmm27 parameters

Hi, On Sat, Apr 11, 2015 at 1:06 PM, Stavros Chatzieleftheriou < stavros...@windowslive.com> wrote: > Dear all, > I am new to Gromacs and I have a simple question. How can I get the exact > force field parameters used for my .pdb file (i.e. kb and bo for bonded > terms, kth and tho for angle term

Re: [gmx-users] Post-Processing on the REMD trj

On Tue, Apr 14, 2015 at 2:50 AM, 14110220...@fudan.edu.cn < 14110220...@fudan.edu.cn> wrote: > Dear users, > > Rescently, I used REMD to do some simulation by Gromacs , I konw GROMACS > exchanges coordinates. So does this means every trajectory was written at a > temperture ?AND if i want to analy

Re: [gmx-users] How to call an external LAPACK function in gromacs

Hi, When you ran cmake originally, what did it report about which LAPACK it found and will use? (You may need to clean your build tree and start again in order to find this out.) What is the linker command line now (e.g. make VERBOSE=1) Mark On Mon, Apr 13, 2015 at 11:30 PM, qian wang wrote: >

Re: [gmx-users] adding SR2++ to charm27 force field

Hi, Inspect the whole output. Is pdb2gmx picking up the version of charmm27 you think it is? Mark On Tue, Apr 14, 2015 at 8:40 AM, Ming Tang wrote: > Dear all, > > I am trying to add SR 2++ in charm27 force field. I modified the > ffnonbonded.itp, ffnanonbonded.itp, ions.itp, aminoacids,rtp, a

Re: [gmx-users] Number of hardware threads does not match OpenMP

On Tue, Apr 14, 2015 at 8:58 AM, Dries Van Rompaey < dries.vanromp...@gmail.com> wrote: > Dear Szilárd, > > Thanks for your reply. I'll try your proposed fix. > I was also wondering if the simulations performed could be affected in > terms of reliability and accuracy or not (ie. do I need to redo

Re: [gmx-users] How to add a repulsive harmonic potential

>Depending on how structurally complex the ligands are, it may be very easy to >define a dummy atom within the structure using a virtual site, then specifying >a >nonbonded interaction only between these virtual sites using [nonbond_params]. >That way, these sites will not affect ligand-water,