[gmx-users] g_fg2cg

Dear XAvier Thank you very much from your response. Yes, I defined mapping in atomistic topology as: [mapping ]   1   1    2    3    4    5  6 because for butanole we have one bead. Please help me. Best Regards Dina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.

Re: [gmx-users] how to add custom potential function

On 7/03/2012 2:07 PM, smith bill wrote: i have three custom potential functions to add into gromacs,what's the easiest way to do this? Don't. :-) Use custom lookup tables. See various manual sections. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/l

[gmx-users] how to add custom potential function

i have three custom potential functions to add into gromacs,what's the easiest way to do this? -- 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! Pl

Re: [gmx-users] g_fg2cg

Did you define the mapping in the atomistic topology? On Mar 6, 2012, at 10:57, dina dusti wrote: > Dear Gromacs Specialists, > > I have one problem about g_fg2cg. I want convert structure of butanole in fg > to cg by g_fg2cg, but I take this error: > > "Program g_fg2cg, VERSION 3.3.1 > S

Re: [gmx-users] g_sdf -> and g_spatial

Dallas Warren wrote: I know, bit of a zombie topic (May 2011) to be digging out of the archives here. I have previously used g_sdf rather extensively and needed to generate some spatial distribution functions for a paper. Started to looked into g_spatial to see if that can do what I want it t

[gmx-users] g_sdf -> and g_spatial

I know, bit of a zombie topic (May 2011) to be digging out of the archives here. I have previously used g_sdf rather extensively and needed to generate some spatial distribution functions for a paper. Started to looked into g_spatial to see if that can do what I want it to, since g_sdf has been

Re: [gmx-users] Gromacs 3.3.3 on Lion Xgrid

dtrace and see what it's trying to exec? I have a feeling that it's due to Xcode shipping with LLVM trying to emulate GCC and something doesn't like it. On 2012-03-06 09:03:34PM +, Benjamin Hall wrote: > Hi > > I realise this is a question regarding an old version of gromacs on a new OS, >

[gmx-users] Gromacs 3.3.3 on Lion Xgrid

Hi I realise this is a question regarding an old version of gromacs on a new OS, but I was hoping that someone could tell me why grompp might fail in 3.3.3 with the following error llvm-gcc-4.2: error trying to exec 'i686-apple-darwin10-llvm-gcc-4.2': execvp: No such file or directory In part

Re: [gmx-users] Inconsistent shifts - is it something wrong with pbc

Hi Justin, Really appreciate your help. I have solved the problem following your suggestion :) I love this community~ 2012/3/7 Justin A. Lemkul > > > ming ma wrote: > >> Hi, >> >> Thanks for looking at this email. Before I asked this question, I have >> read most of the related topics in gromac

Re: [gmx-users] Inconsistent shifts - is it something wrong with pbc

ming ma wrote: Hi, Thanks for looking at this email. Before I asked this question, I have read most of the related topics in gromacs's mailing list, but still can't solve it. When I was trying to do energy minimization of graphene with pbc, I got several messages "there are # inconsistent s

[gmx-users] Inconsistent shifts - is it something wrong with pbc

Hi, Thanks for looking at this email. Before I asked this question, I have read most of the related topics in gromacs's mailing list, but still can't solve it. When I was trying to do energy minimization of graphene with pbc, I got several messages "there are # inconsistent shifts, check your topo

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

Lara Bunte wrote: Hi In some lines the equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like [ angles ] ; aiajak functc0c1c2c3 2 119 1123.75 250.00

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

Lara Bunte wrote: Hi After pdb2gmx are in the [ angles ] section some lines missing and I am pretty sure that they are defined in my .rtp file in my force field folder. There are also just a few lines mission, most of the angles are in topology. I know the parameters so I can add it by hand to

[gmx-users] Missing Interactions in [ angles ] Section in Topology

Hi After pdb2gmx are in the [ angles ] section some lines missing and I am pretty sure that they are defined in my .rtp file in my force field folder. There are also just a few lines mission, most of the angles are in topology. I know the parameters so I can add it by hand to topology but what

Re: [gmx-users] Two [ dihedrals ] Sections in Topology

Lara Bunte wrote: Hi After pdb2gmx I got two [ dihedrals ] sections in the topology file. [ dihedrals ] aiajakal functc0c1c2 c3c4c5 2 119 8 5 6 8 910 5 6 8

[gmx-users] Two [ dihedrals ] Sections in Topology

Hi After pdb2gmx I got two [ dihedrals ] sections in the topology file. [ dihedrals ]   ai    aj    ak    al funct    c0    c1    c2    c3    c4    c5     2 1    19 8 5     6 8 9    10 5     6 8    19 1 5 [ di

Re: [gmx-users] [ pairs ] section in topology

Lara Bunte wrote: Hi My topology file which I get after pdb2gmx has in one section following section: [ pairs ] ; aiaj functc0c1c2c3 1 5 1 1 6 1 1 9 1 117 1 Is it correct that there are no e

[gmx-users] [ pairs ] section in topology

Hi My topology file which I get after pdb2gmx has in one section following section: [ pairs ] ;  ai    aj funct    c0    c1    c2    c3     1 5 1     1 6 1     1 9 1     1    17 1 Is it correct that there are no entries in c0, c1, c2 a

[gmx-users] g_fg2cg

Dear Gromacs Specialists, I have one problem about g_fg2cg. I want convert structure of butanole in fg to cg by g_fg2cg, but I take this error: "Program g_fg2cg, VERSION 3.3.1 Source code file: gmxfio.c, line: 735 Range checking error: Variable fio has value -1. It should have been within [ 0 .

Re: [gmx-users] grompp - Invalid command line argument

Lara Bunte wrote: Hi I used the command grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr and got the error Source code file: /home/adrian/src/gromacs-4.5.5/src/gmxlib/statutil.c, line: 819 Invalid command line argument: em.tpr What is the problem here? The command posted ab

[gmx-users] grompp - Invalid command line argument

Hi I used the command grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr and got the error Source code file: /home/adrian/src/gromacs-4.5.5/src/gmxlib/statutil.c, line: 819 Invalid command line argument: em.tpr What is the problem here? Greetings Lara -- gmx-users mailing listgm

Re: [gmx-users] tpbconv to extend a simulation

Juliette N. wrote: Hello all, I read the online instruction on how to extend a run. I just wanted to double check the procedure because of the NOTE below after issuing tpbconv –f old.trr -s old.tpr -e old.edr -o old-extend.tpr -until 1 NOTE: Reading the state from trajectory is an obsole

[gmx-users] tpbconv to extend a simulation

Hello all, I read the online instruction on how to extend a run. I just wanted to double check the procedure because of the NOTE below after issuing tpbconv –f old.trr -s old.tpr -e old.edr -o old-extend.tpr -until 1 NOTE: Reading the state from trajectory is an obsolete feaure of tpbconv.  

[gmx-users] Helix - Ligand binding - mimic stability

Dear Gmx Users, I am wondering your approach for such system: Ligand binding alpha helix which is a part of big helical bundle - in reality the conformation is rather stable. I want to use position restrained dynamics - surely for terminal residues and possibly for the residue in the middle? (the

Re: [gmx-users] one ligand in ATB

Hey Ahmet, The conformation is not important. What is important is that the number and order of the atoms in you structure match the topology file. If the order is wrong, you can simply swap lines to make them match. If the number of atoms is different, you have to fix your structure to be able to

[gmx-users] one ligand in ATB

Hi, I have a pdb file containing only one ligand. There is already .gro and .itp files of this ligand at Automated Topology Builder (ATB). I want to use the gro and .itp files of this ligand from ATB. The ligand coordinates in my pdb file is different than at ATB. i.e. ATB have used another coordi

Re: [gmx-users] Coupling groups

On Tue, Mar 6, 2012 at 11:44 AM, Mark Abraham wrote: > On 6/03/2012 10:40 PM, Steven Neumann wrote: > > > > On Tue, Mar 6, 2012 at 11:35 AM, Mark Abraham wrote: > >> On 6/03/2012 8:21 PM, Steven Neumann wrote: >> >>> Dear Gmx Users, >>> I am running my protein with ligand. at the begining of my

Re: [gmx-users] Coupling groups

On 6/03/2012 10:40 PM, Steven Neumann wrote: On Tue, Mar 6, 2012 at 11:35 AM, Mark Abraham > wrote: On 6/03/2012 8:21 PM, Steven Neumann wrote: Dear Gmx Users, I am running my protein with ligand. at the begining of my simulation th

Re: [gmx-users] Coupling groups

On Tue, Mar 6, 2012 at 11:35 AM, Mark Abraham wrote: > On 6/03/2012 8:21 PM, Steven Neumann wrote: > >> Dear Gmx Users, >> I am running my protein with ligand. at the begining of my simulation the >> protein is far away from the ligand. Then in about 5-10 ns my ligand binds >> to the protein surf

Re: [gmx-users] Coupling groups

On 6/03/2012 8:21 PM, Steven Neumann wrote: Dear Gmx Users, I am running my protein with ligand. at the begining of my simulation the protein is far away from the ligand. Then in about 5-10 ns my ligand binds to the protein surface remaining there for rest 90-95 ns. Would you adjust coupling g

Re: [gmx-users] g_bar bug with temperature

On 6/03/2012 6:58 PM, Tom Kirchner wrote: Dear all, I made a free energy calculation and want to evaluate my data with g_bar. But when I am using g_bar on my .xvg files I get an error of the form: Temperature in file md_0.35.xvg different from earlier files or setting All simulations we

[gmx-users] g_bar bug with temperature

Dear all, I made a free energy calculation and want to evaluate my data with g_bar. But when I am using g_bar on my .xvg files I get an error of the form: Temperature in file md_0.35.xvg different from earlier files or setting All simulations were performed at temperature 298.15 K, this nu