Re: [gmx-users] simulation_time[Nikita Bora]

hi... So there is no direct way to know the values to be used . however the last line is still unclear... Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Fri, May 20, 2016 at 12:00 PM, Tsjerk Wassenaar wrote: > Hi Nikita, > > It's not like there's a range to t

[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 fi

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] 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 we

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 > wrote: > > On OSX 11.

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 -

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: > > ./deviceQuery Starting... > > CUDA Device Query (Runti

[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 ty

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 s

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 N

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) > > Device 0: "GeForce GTX 680" >

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 should be in the same [atom

[gmx-users] restraints between two different molecules

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 should be in the same [atomtype] section (which is not the case) and also something related to the u

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 t

[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 wit

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

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] 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 ffnonbonded.itp in Amber ff.

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 thei

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 they are already for io

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 i

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: > Hi all, > > i nee

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 f

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 spherocyli

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 prot

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 e

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 for ions. can anyone t

[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 orde

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 wrote:‬ > Hi >

[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 minimization

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] 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

[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 -DCUDA_TOOLKIT_ROOT_D

[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 >