[gmx-users] Freezing the solute

Hi, I would like to run a simulation with a frozen solute. The manual suggests to add the following to the MDP: freezegrps SOLUTE freezedim Y Y Y And creating an index group called SOLUTE. I did this but I can still some atoms of SOLUTE moving during the minimization. What could

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 153, Issue 73

Dear Justin, Thank you very much for quick response. I want to capitalize cn9, but I could not find small cn9 in my force field. There is CN9 (capital) only for DNA. There is not any DNA molecules in my system. Best regards, Mijiddorj > > On 1/15/17 11:04 PM, Mijiddorj Batsaikhan wrote: >

Re: [gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27

Dear Justin, Thank you very much for quick response. I want to capitalize cn9, but I could not find small cn9 in my force field. There is CN9 (capital) only for DNA. There is not any DNA molecules in my system. Best regards, Mijiddorj On 1/15/17 11:04 PM, Mijiddorj Batsaikhan wrote: > Dear

Re: [gmx-users] PREPARING THE RESIDUE TOPOLOGY FILE

On 1/16/17 12:04 AM, Subashini .K wrote: Hi, I am learning to prepare the residue topology file (.rtp file) . While preparing the file, what does the third and fourth column describe? This is the example of methane. What do the numbers -0.240 and 1 convey? Similarly 0.060 and 1? [

Re: [gmx-users] Regarding topology...

On 1/16/17 2:44 AM, Dilip H N wrote: My questions are.. 1] how to create a topology file for ammonia.?? 2] how to create a force field for ammonia, what is the residue name for ammonia in .pdb file.?? 3] Why ammonia.itp is not there in gromacs..?? 4] Which force field to choose for

Re: [gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27

On 1/16/17 4:02 AM, Mijiddorj Batsaikhan wrote: Dear Justin, Thank you very much for quick response. I want to capitalize cn9, but I could not find small cn9 in my force field. There is CN9 (capital) only for DNA. There is not any DNA molecules in my system. The error you posted before

[gmx-users] CLARIFICATION IN RESIDUE TOPOLOGY FILE

Hi gromacs users, While preparing the .rtp file, what does the third and fourth column describe? ; Methane [ CH4 ] [ atoms ] C opls_138-0.240 1 H1 opls_140 0.060 1 H2 opls_140 0.060 1 H3 opls_140 0.060 1 H4 opls_140 0.060 1

Re: [gmx-users] Regarding topology...

when the command is given gmx pdb2gmx -f ammonia.pdb -o ammonia.gro , it says as fllows... Select the Force Field: >From '/usr/local/gromacs/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS

Re: [gmx-users] CLARIFICATION IN RESIDUE TOPOLOGY FILE

On Tue, Jan 17, 2017 at 3:55 AM Subashini .K wrote: > Hi gromacs users, > > > While preparing the .rtp file, what does the third and fourth column > describe? > > ; Methane > [ CH4 ] > [ atoms ] > > > C opls_138-0.240 1 > > H1 opls_140 0.060 1 > >

Re: [gmx-users] Regarding topology...

Thank you Justin... 1] I have created an Ammonia molecule from Avogadro software...and saved it in .pdb file format... 2] Than gave the command gmx pdb2gmx -f ammonia.pdb -o ammonia.gro 3] There im not getting the CGenFF force field/r CHARMM36 port..., my gromacs version is 5.0.7.., How to

[gmx-users] European Hardware Vendors

Hello, I am writing a short proposal for a potential postdoc position. I would like to include a quote for a decent computer system to run these types of simulations. However, I know that purchasing equipment for European Universities is quite difficult. Would any of you know some reliable

Re: [gmx-users] Pulling Mechanics

On 1/13/17 6:37 PM, Alexander Yang wrote: > > Hi everyone, > > > > I am pulling a water molecule into a bilayer using an absolute reference > > (mdp file below). I have tried to adapt methodology in Justin Lemkul's > > umbrella sampling tutorial, but I have encountered a couple issues: > > > > If

[gmx-users] temperature coupling groups for homogeneous mixtures/ ionic liquids?

Dear Gromacs Users, I am simulating ionic liquids and the mixtures of ionic liquids and neutral solvents. I used Berendsen or Nose-Hoover temperature coupling for NPT systems. No constrains or restrains are in the system. I just find these discussions and documentations about the temperature

Re: [gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27

... and please suggest a correction to whoever distributed such a non-conforming parameter set. Mark On Mon, Jan 16, 2017 at 7:45 PM Justin Lemkul wrote: > > > On 1/16/17 4:02 AM, Mijiddorj Batsaikhan wrote: > > Dear Justin, > > > > Thank you very much for quick response. > >

Re: [gmx-users] temperature coupling groups for homogeneous mixtures/ ionic liquids?

Hi, yes it matters. In general tc-grps=system is better/correct, unless the thermal energy transfer across your system is hampered (e.g. a lipid membrane, or a large protein). It hasn't changed with versions. In addition, the Berendsen thermostat produces the wrong ensemble. To check previous

Re: [gmx-users] Freezing the solute

Hi, If you think frozen atoms are moving, then you didn't define frozen groups the way you intended. Mark On Mon, Jan 16, 2017 at 9:35 AM Jernej Zidar wrote: > Hi, > I would like to run a simulation with a frozen solute. The manual > suggests to add the following to