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] 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

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 > >

[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] 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] 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] 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

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] 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

[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] 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

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] 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] 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: >

[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