Re: [gmx-users] Re: inconsistent energies

On 8/01/2011 1:38 PM, Vlad Isaev wrote: Thanks, Mark. No, it is not picking any chk files. But the coordinates in the gro file after mdrun change slightly for some of the atoms on using cg and l-bfgs, whereas with steep they remain the same. OK, well this must be a consequence of the algorit

[gmx-users] Re: inconsistent energies

Thanks, Mark. No, it is not picking any chk files. But the coordinates in the gro file after mdrun change slightly for some of the atoms on using cg and l-bfgs, whereas with steep they remain the same. e.g., in b4min.gro submitted to cg or l-bfgs or steep: 2GLY O 13 0.736 0.922 -0.35

Re: [gmx-users] justin

On 07/01/11 17:00, mustafa bilsel wrote: Justin, Are you sure? I installed 4.5.3 and tried Methanol, MTH, MeOH. Nothing changed. I suggest you to try it by yourself. Don't try to remind people the help rules. JUST HELP OR DONOT HELP. We're not at your orders and shouting at people who try to

gmx-users@gromacs.org

Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, January 10, 2011. For all questions about CloudBroker, please contact the compan

Re: [gmx-users] g_msd Utility - (Unexpected) Different Results Depending on Output Flag

On 6/01/2011 2:03 AM, Solomon Berman wrote: Greetings friends! I have a question this morning about the g_msd utility related to the output generated by different flags. I'm working with an LJ Liquid and am trying to determine the diffusion constant for the system. I'm employing both the Ein

Re: [gmx-users] Ion-Clustering?

On 8/01/2011 12:56 AM, Micholas Smith wrote: Hello everyone, I've been performing some rather long simulations (400ns) of a short peptide chain in explicit TIP4P water solvent using opls-aa forcefield with ionic concentrations near 1M, and I am finding a lot of "clustering" of my ionic specie

Re: [gmx-users] inconsistent energies

On 8/01/2011 12:10 AM, Vlad Isaev wrote: Hi, I want to calculate the energy of a peptide. No minimization, or md, just the energy at 0 K. I use this input: integrator = steep nsteps = 0 nstenergy= 1 nstlist = 0 ns_type

[gmx-users] Re: XTC file not being created, while TRR file is

> > Hi João, I don't remember EM runs ever producing .xtc files, maybe to > > prevent people to use them when "grompp'ing" in the next step. (they're at > much lower precision) > > Anyway, that would be nice in case you want to see what's going on during > EM. > > Thanks for the answer Diego, indee

Re: [gmx-users] When will FEP be on GPU?

Hi, Currently there is no concrete plan to implement FEP on GPUs. AFAIK there is an OpenMM plugin which could be integrated, but I surely don't have time to work on that and I don't know of anyone else working on it. Contribution would be welcome, though! Regards, -- Szilárd On Thu, Nov 11, 20

[gmx-users] 4. Requesting advice on pressure scaling in a protein-in-membrane system. (Daniel Adriano Silva M)

ion: On this step I had frozen the Protein and excluded the > Protein-Protein energy. > > Thanks, > Daniel Silva > -- next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110107/b897663b/atta

Re: [gmx-users] XTC file not being created, while TRR file is

Hi João, I don't remember EM runs ever producing .xtc files, maybe to prevent people to use them when "grompp'ing" in the next step. (they're at much lower precision) Anyway, that would be nice in case you want to see what's going on during EM. On Fri, Jan 7, 2011 at 7:02 PM, João Rodrigues wro

[gmx-users] XTC file not being created, while TRR file is

Hello all, I'm trying to run energy minimization on my system (protein complex). Since it's a bit big (produces 2GB of trr files using l-bfgs) I'm trying to supress most of this output and replace the trr file with an xtc file. I'm using these options in my mdp file (output related): nstxout

Re: [gmx-users] justin

mustafa bilsel wrote: Justin, Are you sure? I installed 4.5.3 and tried Methanol, MTH, MeOH. Nothing changed. I suggest you to try it by yourself. I did, and it works quite nicely. Don't try to remind people the help rules. JUST HELP OR DONOT HELP. I guess attempting to guide you to mo

[gmx-users] justin

Justin, Are you sure? I installed 4.5.3 and tried Methanol, MTH, MeOH. Nothing changed. I suggest you to try it by yourself. Don't try to remind people the help rules. JUST HELP OR DONOT HELP. mustafa This topology defines the [moleculetype] name as "Methanol," which is the name that needs to

Re: [gmx-users] trjconv with multiple chains

On 07/01/11 02:17, yuanyuan wang wrote: dear all, I am doing a simulation that have many chains in a box , and I can find a center for them after serval tries. I use almost every option of trjconv,-pbc mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box

Re: [gmx-users] Requesting advice on pressure scaling in a protein-in-membrane system.

Daniel Adriano Silva M wrote: Dear gmx users and developers, I am facing a problem that is new for me and I will appreciate advice from your expertise. I am working with a big protein complex (around 100K atoms, several subunits) and I used g_membed to embed it in a (aprox 24 14 nm) pre-equ

[gmx-users] Requesting advice on pressure scaling in a protein-in-membrane system.

Dear gmx users and developers, I am facing a problem that is new for me and I will appreciate advice from your expertise. I am working with a big protein complex (around 100K atoms, several subunits) and I used g_membed to embed it in a (aprox 24 14 nm) pre-equilibrated POPC membrane, however afte

Re: [gmx-users] To make continuous trj in REMD

Qin Qiao wrote: 2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu>> Qin Qiao wrote: 2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu> >> Qin Qiao wrote: Dear all, I came acr

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

On 8/01/2011 1:09 AM, mustafa bilsel wrote: Daer Justin, I changed the last line as MTH 660 I got the same error, Atomtype CMET not found Do you mean this? Go and look at the molecule name in gromos43a1.ff/methanol.itp and find the name it uses. You *must* use that name in the [molecules] se

[gmx-users] Ion-Clustering?

Hello everyone,I've been performing some rather long simulations (400ns) of a short peptide chain in explicit TIP4P water solvent using opls-aa forcefield with ionic concentrations near 1M, and I am finding a lot of "clustering" of my ionic species. Has anyone else run into this type of problem? I

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

mustafa bilsel wrote: Daer Justin, I changed the last line as MTH 660 I got the same error, Atomtype CMET not found Do you mean this? I already explained to you what the problem was with that error: http://lists.gromacs.org/pipermail/gmx-users/2011-January/057323.html If you ignore the a

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

Daer Justin, I changed the last line as MTH 660 I got the same error, Atomtype CMET not found Do you mean this? best wishes mustafa Message: 1 Date: Fri, 07 Jan 2011 07:04:05 -0500 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Re: methanol simulation error To: Discussion list for GROMAC

Re: [gmx-users] To make continuous trj in REMD

2011/1/7 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >> >>Qin Qiao wrote: >> >>Dear all, >> >>I came across a problem when I want to make the REMD >>trajectories continuous. >> >>What I did: >> >

Re: [gmx-users] To make continuous trj in REMD

Qin Qiao wrote: 2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu>> Qin Qiao wrote: Dear all, I came across a problem when I want to make the REMD trajectories continuous. What I did: 1. 'demux.pl REMD_0.log

Re: [gmx-users] To make continuous trj in REMD

2011/1/7 Justin A. Lemkul > > > Qin Qiao wrote: > >> Dear all, >> >> I came across a problem when I want to make the REMD trajectories >> continuous. >> >> What I did: >> >> 1. 'demux.pl REMD_0.log' --to get the >> 'replica_index.xvg' >> >> 2. 'trjcat -f ../REMD_*.xtc -

[gmx-users] inconsistent energies

Hi, I want to calculate the energy of a peptide. No minimization, or md, just the energy at 0 K. I use this input: integrator = steep nsteps = 0 nstenergy= 1 nstlist = 0 ns_type = simple pbc = n

Re: [gmx-users] To make continuous trj in REMD

Qin Qiao wrote: Dear all, I came across a problem when I want to make the REMD trajectories continuous. What I did: 1. 'demux.pl REMD_0.log' --to get the 'replica_index.xvg' 2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux ../replica_index.xvg' It seems smooth

[gmx-users] To make continuous trj in REMD

Dear all, I came across a problem when I want to make the REMD trajectories continuous. What I did: 1. 'demux.pl REMD_0.log' --to get the 'replica_index.xvg' 2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux ../replica_index.xvg' It seems smooth. But when I check the rmsd of the output

Re: [gmx-users] trjconv with multiple chains

Amit Choubey wrote: Make your box bigger? Box size is unrelated to trjconv. Periodicity effects will still apply - things will diffuse no matter how large you try to make the box. -Justin 2011/1/6 yuanyuan wang mailto:yilin3...@126.com>> dear all, I am doing a simulat

Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

Carla Jamous wrote: Thank you, It worked, one last question. Something is not very clear to me: -ov: plots the average angle of a group of angles as a function of time!! What does it mean? Because I'm getting positive and negative values in the same plot. Are these values the values of my

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

mustafa bilsel wrote: ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "gromos43a1.ff/methanol.itp" This topology defines the [moleculetype] name as "Methanol," which is the name that needs to be used in the [molecules] direct

Re: [gmx-users] trjconv with multiple chains

Make your box bigger? 2011/1/6 yuanyuan wang > dear all, > I am doing a simulation that have many chains in a box , and I can > find a center for them after serval tries. > I use almost every option of trjconv,-pbc > mol,atom,res,whole,nojump , -ur compact, -center , -box to go

Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

Yes -ov does give you average angle as a function of time. I am not sure if this answers your question though. amit On Fri, Jan 7, 2011 at 2:40 AM, Carla Jamous wrote: > Thank you, > > It worked, one last question. Something is not very clear to me: > > -ov: plots the average angle of a group o

Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

Thank you, It worked, one last question. Something is not very clear to me: -ov: plots the average angle of a group of angles as a function of time!! What does it mean? Because I'm getting positive and negative values in the same plot. Are these values the values of my dihedral angle as a functi

Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

try the -type option with dihedral amit On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous wrote: > Hi Everyone, > > Please I'm trying to calculate one dihedral angle as a function of time > during my simulation. > For this, I used g_angle. In the manual (version 4.0.3) it says: the > indexfile shoul

Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

On 7/01/2011 9:16 PM, Carla Jamous wrote: Hi Everyone, Please I'm trying to calculate one dihedral angle as a function of time during my simulation. For this, I used g_angle. In the manual (version 4.0.3) it says: the indexfile should contain atom-triplets or atom-quadruplets for dihedrals.

[gmx-users] number of index elements not multiple of 3, these can not be angle triplet

Hi Everyone, Please I'm trying to calculate one dihedral angle as a function of time during my simulation. For this, I used g_angle. In the manual (version 4.0.3) it says: the indexfile should contain atom-triplets or atom-quadruplets for dihedrals. I put an atom-quadruplet in my index file, but

[gmx-users] Re: methanol simulation error

Hi Mark, her is my topology, best wishes mustafa ; ;File 'topol.top' was generated ;By user: onbekend (0) ;On host: onbekend ;At date: Fri Jan 7 00:19:16 2011 ; ;This is a standalone topology file ; ;It was generated using program: ;pdb2gmx - VERSION 4.5.1 ; ;Comma

RE: [gmx-users] Re: [ atomtypes ] are not case sensitive?

Yes. I changed this, since it is required for Amber support with proper atom type names. But I seem to have forgotten to add it to the 4.5 release notes. Berk From: awil...@ebi.ac.uk Date: Thu, 6 Jan 2011 10:23:25 + To: gmx-users@gromacs.org CC: Subject: [gmx-users] Re: [ atomtypes ] ar