Re: [gmx-users] Problem with g_rdf

Excuseme dear Dr. Tomas, forgiveme the boldness, I'm new with this, and I dont know who to address when I have a problem. My name is Hector, and I'm tryng to install the gromacs software in my computer; I follewed all the steps in the online manual, however when I compile Gromacs with the instruc

Re: [gmx-users] Is it possible to use a force filed for Au?

On 2/19/13 5:07 PM, Ali Alizadeh wrote: Dear Justin Thank you for your reply, On 2/19/13 4:57 PM, Ali Alizadeh wrote: Dear All users There are a wall(a gold crystal with 111 orientation) and a bulk of fluid(alkane) in my simulation box, My problem is, Is it possible to use a force file

Re: [gmx-users] Problem with g_rdf

On 2/19/13 5:04 PM, Thomas Schlesier wrote: On 2/19/13 3:10 PM, Thomas Schlesier wrote: > Dear all, > I have a question regarding g_rdf. > My system consits of 10 disacchardids (in the following A-B, with > A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF > (

[gmx-users] Re: gmx-users Digest, Vol 106, Issue 101

Dear Justin Thank you for your reply, > > > On 2/19/13 4:57 PM, Ali Alizadeh wrote: >> Dear All users >> >> There are a wall(a gold crystal with 111 orientation) and a bulk of >> fluid(alkane) in my simulation box, >> >> My problem is, Is it possible to use a force filed for Au? Beside, Can >> I

[gmx-users] Problem with g_rdf

On 2/19/13 3:10 PM, Thomas Schlesier wrote: > Dear all, > I have a question regarding g_rdf. > My system consits of 10 disacchardids (in the following A-B, with > A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF > (with flag '-rdf mol_com')for A-A, B-B and the inter

Re: [gmx-users] Is it possible to use a force filed for Au?

On 2/19/13 4:57 PM, Ali Alizadeh wrote: Dear All users There are a wall(a gold crystal with 111 orientation) and a bulk of fluid(alkane) in my simulation box, My problem is, Is it possible to use a force filed for Au? Beside, Can I use two force field at the same time? You need a self-con

Re: [gmx-users] Problem with g_rdf

On 2/19/13 3:10 PM, Thomas Schlesier wrote: Dear all, I have a question regarding g_rdf. My system consits of 10 disacchardids (in the following A-B, with A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF (with flag '-rdf mol_com')for A-A, B-B and the intermolekular

[gmx-users] Problem with g_rdf

Dear all, I have a question regarding g_rdf. My system consits of 10 disacchardids (in the following A-B, with A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for A-B A-A and B-B is no problem. But fo

Re: [gmx-users] NO velocities for ligand

On 2/19/13 2:39 PM, amna khan wrote: hello sir, i want to ask you i have GNERATED the ligand topolagy file by ATB and converting the optimized pdb to gro by editconf, it doesnot generated the volecities for ligand , why is this ? Because editconf has no business generating velocities. V

[gmx-users] Re: Diagonalizing matrix (g_covar)

I'm trying to obtain eigenvalues as well as eigenvectors from the matrix by diagonalizing it. I don't know, is there a way to simplify the problem? How about scalapack or mkl? I heard that those two pose same problems as well. Thank you. -- View this message in context: http://gromacs.5086

Re: [gmx-users] ATP all-atom FF in GROMACS (CHARMM36?)

On 2/19/13 1:29 PM, Bryan Roessler wrote: Hello, I am trying to locate an all-atom FF for ATP that I can use in GROMACS. The ATP residue is stored in a toppar stream file in CHARMM, thus it is not included in the download on the user-submission page for FFs. It also appears that it is not avai

Re: [gmx-users] trjconv woes (broken molecules)

On 2/19/13 1:28 PM, Ignacio Fernández Galván wrote: Hi all, I have a simulation with a frozen molecule which stays around the origin, and a number of solvent molecules with pbc. Due to the way the simulation cell is defined, with a corner at the origin, by default my frozen molecule appears

[gmx-users] ATP all-atom FF in GROMACS (CHARMM36?)

Hello, I am trying to locate an all-atom FF for ATP that I can use in GROMACS. The ATP residue is stored in a toppar stream file in CHARMM, thus it is not included in the download on the user-submission page for FFs. It also appears that it is not available in the AMBER forcefields. It is however

[gmx-users] trjconv woes (broken molecules)

Hi all, I have a simulation with a frozen molecule which stays around the origin, and a number of solvent molecules with pbc. Due to the way the simulation cell is defined, with a corner at the origin, by default my frozen molecule appears broken, a piece on every corner of the box, and I want

Re: [gmx-users] rtp topology file for ligand

On 2/19/13 12:53 PM, amna khan wrote: i generated the ligand.gro by using the command *editconf -g my_otp_ligand.pdb -o ligand.gro* * * *WARNING: all CONECT records are ignored* *Read 38 atoms* *No velocities found* it printed this and after this i did as mention in tutorial it generated the

Re: [gmx-users] rtp topology file for ligand

i generated the ligand.gro by using the command *editconf -g my_otp_ligand.pdb -o ligand.gro* * * *WARNING: all CONECT records are ignored* *Read 38 atoms* *No velocities found* it printed this and after this i did as mention in tutorial it generated the bad box error and the wc -l comand resul

Re: [gmx-users] Dihedral angel

On 2/19/13 10:52 AM, 라지브간디 wrote: I want to calculate the dihedral angel of side chain of Arginine. could you tell how it can be done? how do i create ndx for Arg and look at the dihedral angel in sinumation time point ? g_angle will measure the dihedral. Refer to g_angle -h for available

Re: [gmx-users] rtp topology file for ligand

On 2/19/13 10:53 AM, amna khan wrote: yes i am following this tutorial too this is my topology file for the ligand i made by atb *http://compbio.biosci.uq.edu.au/atb/download.py?molid=7045 * *from here i got the .itp file and optimzed ligand.pdb file but what about the .gro file and .top fil

[gmx-users] Dihedral angel

I want to calculate the dihedral angel of side chain of Arginine. could you tell how it can be done? how do i create ndx for Arg and look at the dihedral angel in sinumation time point ? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Ple

Re: [gmx-users] rtp topology file for ligand

yes i am following this tutorial too this is my topology file for the ligand i made by atb *http://compbio.biosci.uq.edu.au/atb/download.py?molid=7045 * *from here i got the .itp file and optimzed ligand.pdb file but what about the .gro file and .top file * *i ran that command to make the .gro a

Re: [gmx-users] comm-grps

On 2/19/13 9:25 AM, fciocco wrote: Hi I want to study the interaction between a peptide and a lipid bilayer, with the peptide initialy outside de bilayer. Is correct to choose only "bilayer" and "SOL_ions" as comm-groups ? because grompp complain about that with a warning: some atoms are not

Re: [gmx-users] Ethanolamine force-field parameters missing in charmm27.ff

On 2/19/13 9:41 AM, jneeraj wrote: Hello, I plan to run a MD on a protein + ethanolamine (ETAM) system using Gromacs ver 4.5.5 with charmm27 force-field. Though charmm27 force-field (top_all27_prot_lipid.inp, also see http://users.mccammon.ucsd.edu/~rlaw/top_all27_prot_lipid.inp.htm

Re: [gmx-users] NVT and NPT Equalibration

On 2/19/13 10:07 AM, Sainitin Donakonda wrote: Hi all, I want simulate my protein ligand complex for 20 nanoseconds..(final production run) So i set up NVT and NPT equlibrations for 200 ps each.. Can anyone tell me is this correct ? to setup 200 ps prior to 20 ns MD production? There is n

Re: [gmx-users] cmaptypes format

Thank you so much 2013/2/19 Per Larsson > Hi Francesco > > That number corresponds to a type for each cmap-entry. The idea (iirc, it > was some time ago) was that it could be useful to be able to have multiple > cmap-types (other grid values, different grid spacing etc) for the same > cmap-dihe

Re: [gmx-users] cmaptypes format

Hi Francesco That number corresponds to a type for each cmap-entry. The idea (iirc, it was some time ago) was that it could be useful to be able to have multiple cmap-types (other grid values, different grid spacing etc) for the same cmap-dihedral (much like different torsions etc...), but base

[gmx-users] Ethanolamine force-field parameters missing in charmm27.ff

Hello, I plan to run a MD on a protein + ethanolamine (ETAM) system using Gromacs ver 4.5.5 with charmm27 force-field. Though charmm27 force-field (top_all27_prot_lipid.inp, also see http://users.mccammon.ucsd.edu/~rlaw/top_all27_prot_lipid.inp.htm

[gmx-users] comm-grps

Hi I want to study the interaction between a peptide and a lipid bilayer, with the peptide initialy outside de bilayer. Is correct to choose only "bilayer" and "SOL_ions" as comm-groups ? because grompp complain about that with a warning: some atoms are not part of any center of mass motion remov

Re: [gmx-users] terminal phosphate residue for dna simulations

Hi Vedat First of all, the coordinates input file (for instance, pdb) must have terminal nucleotides with "free", dangling phosphate groups. In most of the cases, such terminal phosphates are absent. If the structure indeed has these phosphates, it is possible to simulate a mono-, oligo- or polynu

Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

Hi, Thanks All for help. Now is working! Best! tomek On Tue, Feb 19, 2013 at 2:38 PM, Mark Abraham wrote: > but this I got also with gromacs 4.5.5 which is running ok so I think this > > > is not a problem in my case. > > > > Like Alexey notice the problem is that my nodes have different > >

[gmx-users] terminal phosphate residue for dna simulations

hi guys, does anyone know about a way to simulate mono- or polynucleotides along with a 3' or 5' bound monophosphate using an amber force field like ffamber99sb? i couldn't find any residue definition for a terminal phosphate group such as " P3' " or " P5' " (exemplarily). do they indeed not

Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

but this I got also with gromacs 4.5.5 which is running ok so I think this > is not a problem in my case. > > Like Alexey notice the problem is that my nodes have different > architecture.. but this was not a problem with gromacs 4.5.5 > Yes, that is expected. Probably both machines support SSE2,

Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

Hi Tomek, Gromacs 4.6 uses very different accelerated kernels to 4.5.5. These are hardware specific and you must therefore select acceleration appropriate for your hardware. your login node will automatically use and select AVX-128-FMA acceleration. However, your compute nodes are considerab

Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

On Tue, Feb 19, 2013 at 1:32 PM, Tomek Wlodarski wrote: > The problem is that this is only message I got... But that's an important error. GROMACS 4.6 depends a lot on the compiler generated code, as opposed to 4.5 and previous which used hand-written assembler code. The build procedure detects t

Re: [gmx-users] error in editconf

On 2/19/13 4:53 AM, az kalsom wrote: hi all, i generated the ligand topology file by prodrg server and then i generated the .out file from gaussain software aund used itp adjuster to adjsut the charges in ligand itp file but still i am getting the bad box error when i run the editconf command

Re: [gmx-users] There was 1 error in input file(s)

On 2/19/13 4:29 AM, 라지브간디 wrote: Dear GMX users, I have done nvt part and then start to do npt part for my protein but it shows error like Fatal error: There was 1 error in input file(s) Please how can avoid this? Fix the error :) In seriousness, no one can help you unless you provid

Re: [gmx-users] rtp topology file for ligand

On 2/19/13 4:23 AM, amna khan wrote: hi all, i generated the .itp file for my ligand using ATB, and i have generated the protein topology file by using the forcefield 13 my question is i need to generate the *ligand .top and .gro files* and when i use the command *pdb2gmx -f lig.pdb -o

Re: [gmx-users] Re: A note while running grompp for nvt equilibration

On 2/19/13 1:36 AM, Anu Chandran wrote: Sir, Thank you for the reply. As per the suggestion, I tried increasing the rlist. Note or warning stopped when rlist was increased to 1.8. Also with this value of rcoulomb, the box size also needs to be increased. I would like to know whether it is fine

Re: [gmx-users] Re: vaccum simulation error

Ponder this: What is the pressure of vacuum? On Feb 19, 2013, at 12:32 PM, raji wrote: for vacuum simulation , no need to specify cut-offs right. am using 8x8x8 box and if we don't specify barostat it will again be a NVT simulations right. vacuum simulations can be done only in NVT ?? sorry

Re: [gmx-users] Gromacs 4.6 crushes in PBS queue system

Hi All, The problem is that this is only message I got... I also get this Warning: -- WARNING: Open MPI will create a shared memory backing file in a directory that appears to be mounted on a network filesystem. Creating the

Re: [gmx-users] Re: vaccum simulation error

Have you maybe tried this? http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List/Search?q=%22vacuum+simulation%22 Own initiative and discrete thinking is mandatory for research. On 02/19/2013 12:32 PM, raji wrote: for vacuum simulation , no need to specify cut-offs right. am using 8x8x8

[gmx-users] Re: vaccum simulation error

for vacuum simulation , no need to specify cut-offs right. am using 8x8x8 box and if we don't specify barostat it will again be a NVT simulations right. vacuum simulations can be done only in NVT ?? sorry if am wrong . please clarify this doubt thanks in advance -- View this message in context:

Re: [gmx-users] vaccum simulation error

Using a barostat for vaccum simulations is very peculiar. Erik On Feb 19, 2013, at 10:55 AM, Rajalakshmi.C wrote: hi all, i am trying to simulate polymer chains in solvent and vacuum media using 45a3 forcefield. for vacuum simulation i used different md parameters than that of solvent med

Re: [gmx-users] Number of interactions per residue

On Feb 19, 2013, at 10:19 AM, Kavyashree M wrote: Dear users, *When I use g_hbond with -contact and -r 0.4 on C-alpha atoms -* I get the following message - *** Reading frame 0 time 4000.000 Will do grid-seach on 26x

Re: [gmx-users] Number of interactions per residue

Try a more recent versions. There were a bunch of bugfixes since 4.5.3 Erik On Feb 19, 2013, at 10:19 AM, Kavyashree M wrote: Dear users, *When I use g_hbond with -contact and -r 0.4 on C-alpha atoms -* I get the following message -

[gmx-users] vaccum simulation error

hi all, i am trying to simulate polymer chains in solvent and vacuum media using 45a3 forcefield. for vacuum simulation i used different md parameters than that of solvent media. first i put 100ps NVT and then 100ps NPT. i sucessfully got NVT done but for NPT i got following error , WARNING 1 [fi

[gmx-users] There was 1 error in input file(s)

Dear GMX users, I have done nvt part and then start to do npt part for my protein but it shows error like Fatal error: There was 1 error in input file(s) Please how can avoid this? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Pleas

Re: [gmx-users] Number of interactions per residue

Dear users, *When I use g_hbond with -contact and -r 0.4 on C-alpha atoms -* I get the following message - *** Reading frame 0 time 4000.000 Will do grid-seach on 26x26x19 grid, rcut=0.4 Last frame500 time 5000.0