Re: [gmx-users] restraints between two different molecules

Hi, On Wed, May 25, 2016 at 4:11 PM Rebeca García Fandiño wrote: > Dear Gromacs users, > I am trying to apply some distance restraints between two different > molecules in a Gromacs simulation. I have read different things in the > Gromacs list, such as both molecules

[gmx-users] Force Field for amino acid and peptide

Dear Gromacs user, I am going to simulate the binding free energy of some amino acid to a metal surface in aqueous solution and also peptide adsorption behavior into this surface. I know the force field of the surface as well as the better type of water for such a work, but I do not know which

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

On Wed, May 25, 2016 at 12:58 PM, Uliano Guerrini wrote: > On OSX 11.5 I instelled cuda 7.5, compiled samples and when I run: > > ./deviceQuery Starting... > > CUDA Device Query (Runtime API) version (CUDART static linking) > > Detected 1 CUDA Capable device(s) > >

Re: [gmx-users] Surface tension coupling with Parrinello-Rahman algorithm

Dear André, In that publication it is specified the use of semi-isotropic pressure coupling, not the surface-tension option in Gromacs. They were controlling the surface tension applying a different pressure in XY than in Z. But I guess it still different from my question, which is related to the

Re: [gmx-users] a suitable forcefield for ions

Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can I use them for ions or they are already for ions? eg. for Na sigma= 0.332 and epsilon=0.0115. Does it mean that we can use thIS sigma and epsilon for Na+? On Wed, May 25, 2016 at 2:11 PM, mah maz wrote:

Re: [gmx-users] a suitable forcefield for ions

Thanks Justin. I can only find atoms in ffnonbonded.itp in Amber ff. Where should I search for ions parameters in Amber ff? On Wed, May 25, 2016 at 4:01 PM, mah maz wrote: > Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can > I use them for ions or

Re: [gmx-users] Surface tension coupling with Parrinello-Rahman algorithm

I'd guess it works since it has been done already: http://www.sciencedirect.com/science/article/pii/S0005273613004501 On Wed, May 25, 2016 at 10:31 AM, Giuseppe Léonardo Licari < giuseppe.lic...@unige.ch> wrote: > Dear all, > I have a question concerning the Surface-Tension pressure coupling in

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

> Il giorno 25 mag 2016, alle ore 16:30, Szilárd Páll > ha scritto: > > On Wed, May 25, 2016 at 12:58 PM, Uliano Guerrini > wrote: > On OSX 11.5 I instelled cuda 7.5, compiled samples and when I run: > >

Re: [gmx-users] QMMM grompp error atom numbers fields.

Hi, this is weird. I assume you've put the *'s only in your email? Could you send me (off list) the mdp, index, top and gro file? Perhaps something else, such as missing link atom triggers the error message incorrectly. Gerrit Subject: [gmx-users] QMMM grompp error atom numbers fields.

Re: [gmx-users] Force Field for amino acid and peptide

On 5/25/16 11:05 AM, Alexander Alexander wrote: Dear Gromacs user, I am going to simulate the binding free energy of some amino acid to a metal surface in aqueous solution and also peptide adsorption behavior into this surface. I know the force field of the surface as well as the better type

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

On Wed, May 25, 2016 at 8:20 PM, Uliano Guerrini wrote: > > > Il giorno 25 mag 2016, alle ore 16:30, Szilárd Páll < > pall.szil...@gmail.com> ha scritto: > > > > On Wed, May 25, 2016 at 12:58 PM, Uliano Guerrini < > uliano.guerr...@unimi.it

Re: [gmx-users] gromacs energy minimization fatal error: Invalid bond type 1000 in constant-PH MD

On 5/25/16 9:21 AM, Wang Tao wrote: Hi,Dr Justin! You have mentioned that i missed my itp file.Here is it ## [ moleculetype ] ;molnamenrexcl OHIN 1 [ atoms ] ;id at type res nr residue name at name cg nr charge mass 1opls_434 1OHIN OH 1

[gmx-users] Apply position restraints to part of RNA molecule

Dear gmx users, I am working on simulating a RNA aptamer with GROMACS. I want to apply position restraints to only part of the molecule during equilibration. I created an .itp file including those atoms which I plan to make restrained. I defined position restraints in .mdp file, and in the .top

Re: [gmx-users] Generating topology for a HEM protein with CHARMM27

On 5/25/16 9:58 AM, zeineb SI CHAIB wrote: @Justin, Thank you very much for your help, I finally fixed the problem but I'm having another one with grompp (which was expected): The error that I get is: ERROR 7 [file topol.top, line 41571]: No default Proper Dih. types Fatal error: There

Re: [gmx-users] Combining various Flat-bottomed Potentials

On 5/25/16 1:44 AM, jagannath mondal wrote: Hi I am also interested in the issue of using a flat-bottomed restraint, for a spherocylinder. However, I am not sure whether the current gromacs settings of even a linear combination of a sphere and cylinder can help here to generate a

Re: [gmx-users] Installing GROMACS 5.1.2 om GPU

Hi, You need to follow Intel's instructions for accessing the compiler - including running their magic scripts from each shell that you want to compile from. (Or save yourself some pain, use gcc, and probably run slightly faster.) Mark ‪On Wed, May 25, 2016 at 10:43 AM ‫יוכבד‬‎

Re: [gmx-users] gromacs energy minimization fatal error: Invalid bond type 1000 in constant-PH MD

On 5/25/16 6:06 AM, Wang Tao wrote: Hi,every one! I'm using opls aa in gromacs to conduct constant-PH MD. In my system,PH is equal to 13.There are three kind of groups, NA+,OH- and H2O. The itp file for OH- is created by myself. This is not what constant pH MD is. You've got a fixed

Re: [gmx-users] mdrun terminated with errors with gromacs 5.1 in parallel

Hi, The command /app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi isn't what you used to start the simulation - it couldn't work. Please copy and paste actual things, and do also check out the advice in the install guide about how to get access to installed versions of GROMACS by source GMXRC.

[gmx-users] mdrun terminated with errors with gromacs 5.1 in parallel

Dear Gromacs users, I was trying to do equilibration of a mixed lipid vesicle using gromacs 5.1 in parallel. My pbs script file details for this is the following : /home/lipi/openmpi164/bin/mpirun -np 48 /app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm step6.2_equilibration -rdd 1.8

[gmx-users] gromacs energy minimization fatal error: Invalid bond type 1000 in constant-PH MD

Hi,every one! I'm using opls aa in gromacs to conduct constant-PH MD. In my system,PH is equal to 13.There are three kind of groups, NA+,OH- and H2O. The itp file for OH- is created by myself. After having finished the genbox and genion steps sucessfully, i met a problem in energy

Re: [gmx-users] a suitable forcefield for ions

Hi, Which ions? The monovalent ions commonly used with Amber have a tendency to cluster in unrealistic ways at moderate concentrations if memory serves me right. Kind regards, Erik > On 25 May 2016, at 10:41, mah maz wrote: > > Hi all, > > i need forcefield parameters

[gmx-users] Installing GROMACS 5.1.2 om GPU

Hi I've been having lots of trouble installing gromacs on our GPU machine. I have Intel2015 Compilers on my machine which are identified correctly during configuration. /private/gnss/cmake-2.8.11.2/bin/cmake .. -DCMAKE_INSTALL_PREFIX=/private/gnss/gromacs-5.1.2 -DGMX_GPU=on

[gmx-users] Unusual bond

Dear Gromacs user, The VMD report below warning when I load my minimized ".gro" structure; Warning) Unusual bond between residues: 13724 (none) and 22887 (waters). The VMD does not report any warning when I load my structure "gro" file before energy minimization, but when I minimized it in

Re: [gmx-users] Simulating conjugated protein

On 5/25/16 12:55 AM, Sanket Ghawali wrote: Dear, gmx-users, Hello everyone, I'm simulating a peptide in an SDS micelle, where my peptide is conjugated to a organic compound at the N terminal. The SDS micelle was genrated using CHARMM-GUI, here I am stuck with a problem for adding atom types

[gmx-users] a suitable forcefield for ions

Hi all, i need forcefield parameters for ions. can anyone tell me which forcefield contains ions? can i do ion simulations with amber ff? Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] Unusual bond

On 5/25/16 6:47 AM, Alexander Alexander wrote: Dear Gromacs user, The VMD report below warning when I load my minimized ".gro" structure; Warning) Unusual bond between residues: 13724 (none) and 22887 (waters). The VMD does not report any warning when I load my structure "gro" file before

Re: [gmx-users] a suitable forcefield for ions

On 5/25/16 7:31 AM, mah maz wrote: Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can I use them for ions or they are already for ions? eg. for Na sigma= 0.332 and epsilon=0.0115. Does it mean that we can use thIS sigma and epsilon for Na+? You should spend some time

Re: [gmx-users] a suitable forcefield for ions

Hello team, how can I simulate a protein bind with FE4S4 in gromacs. How to generate the topology. Thank you.. On Wed, May 25, 2016 at 5:12 PM, Justin Lemkul wrote: > > > On 5/25/16 7:40 AM, mah maz wrote: > >> Thanks Justin. I can only find atoms in

Re: [gmx-users] Generating topology for a HEM protein with CHARMM27

@Justin, Thank you very much for your help, I finally fixed the problem but I'm having another one with grompp (which was expected): The error that I get is: ERROR 7 [file topol.top, line 41571]: No default Proper Dih. types Fatal error: There were 13 errors in input file(s) I think that

Re: [gmx-users] a suitable forcefield for ions

On 5/25/16 7:40 AM, mah maz wrote: Thanks Justin. I can only find atoms in ffnonbonded.itp in Amber ff. Where should I search for ions parameters in Amber ff? Every force field has an ions.itp file. Look for those atom types. But knowing those values won't really tell you anything on

Re: [gmx-users] a suitable forcefield for ions

On 5/25/16 8:49 AM, Nilkanta Chowdhury wrote: Hello team, how can I simulate a protein bind with FE4S4 in gromacs. How to generate the topology. Please start a new thread if you have an unrelated question, rather than hijacking someone else's topic. This question has come

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 93

Hi,Dr Justin! You have mentioned that i missed my itp file.Here is it ## [ moleculetype ] ;molnamenrexcl OHIN 1 [ atoms ] ;id at type res nr residue name at name cg nr charge mass 1opls_434 1OHIN OH 1 -1.300 15.999 2opls_435 1

[gmx-users] Surface tension coupling with Parrinello-Rahman algorithm

Dear all, I have a question concerning the Surface-Tension pressure coupling in NPT simulation of a water/dodecane interface. In the Gromacs 5.1 manual it is reported that the coupling of the surface tension to the XY-plane works only with Berendsen algorithm. I tried to do the MD simulation