[gmx-users] pull code in 5.1.2

Hi all, In the Game of Thrones, as soon as you learn characters' names, they get brutally murdered. As soon as I got a good command of the pull code, an mdp working perfectly in 5.0.4 crapped its pants in 5.1.2 (quoted below). The latest manual no longer even has a syntax section for pull

[gmx-users] Deuterium order parameter for POPC/POPS mixed lipid bilayer

Hello Justin, Thank you for your guidance. Regards Kamakshi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests

Re: [gmx-users] Umbrella sampling error with drug molecule

On 3/1/16 7:59 PM, Khuong Truong Gia wrote: Hi all, I am using gromacs to run umbrella sampling simulation with a drug molecule (polymer). I got force field from PRODRG. When run pulling the drug I got this error: step 86530014: Water molecule starting at atom 8336 can not be settled. Check

[gmx-users] Umbrella sampling error with drug molecule

Hi all, I am using gromacs to run umbrella sampling simulation with a drug molecule (polymer). I got force field from PRODRG. When run pulling the drug I got this error: step 86530014: Water molecule starting at atom 8336 can not be settled. Check for bad contacts and/or reduce the timestep if

Re: [gmx-users] Membrane

On 3/1/16 3:02 PM, Abbas Ebadi wrote: Dear Gromacs Users, I'm trying to simulate the permeation of Dendrimer into a DPPC membrane. Whenever I use constraint in my simulations, they interact together easily without any problem. However, when I remove constraint, my system collapse entirely. How

Re: [gmx-users] Membrane

Hi Abbas, Please be more specific. What constraints do you mean? How did you setup the system? What do you mean with 'collapse entirely'? A crash? What does the log file say? Cheers, Tsjerk On Tue, Mar 1, 2016 at 9:02 PM, Abbas Ebadi wrote: > Dear Gromacs Users, > I'm

[gmx-users] Membrane

Dear Gromacs Users, I'm trying to simulate the permeation of Dendrimer into a DPPC membrane. Whenever I use constraint in my simulations, they interact together easily without any problem. However, when I remove constraint, my system collapse entirely. How can I avoid this problem? thanks for your

Re: [gmx-users] Constraining hydrogen - heavy atom bonds with different naming.

On 3/1/16 1:55 PM, Dawid das wrote: Yes of course, but I have already performed a few of simulations. Too bad. I need to repeat them. However, final question. Other atom names can start with M? Of course. -Justin -- == Justin A. Lemkul,

Re: [gmx-users] Constraining hydrogen - heavy atom bonds with different naming.

Yes of course, but I have already performed a few of simulations. Too bad. I need to repeat them. However, final question. Other atom names can start with M? DG -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Constraining hydrogen - heavy atom bonds with different naming.

Oh gosh..., so in that case is there any other way around to constraint those MH11 - MCB1 etc. bond lengths except for renaming all hydrogen atoms? Best wishes, Dawid Grabarek 2016-03-01 19:29 GMT+01:00 Justin Lemkul : > > > On 3/1/16 1:24 PM, Dawid das wrote: > >> Dear Gromacs

Re: [gmx-users] adding mdp to amber99sb

Thanks! On Mar 1, 2016, at 1:16 PM, Justin Lemkul > wrote: On 3/1/16 1:14 PM, Irem Altan wrote: Hi, I am trying to add MPD to the amber99sb forcefields. I have added the necessary things to aminoacids.rtp, aminoacids.hdp, and atomtypes.atp, but when I

Re: [gmx-users] Constraining hydrogen - heavy atom bonds with different naming.

On 3/1/16 1:24 PM, Dawid das wrote: Dear Gromacs Experts, I am pretty sure I have already answered this question long time ago but I cannot find it. What I did is I added a new residue for my system and it contains hydrogen atoms. Now, the thing is that all atoms names start with "M", so I

[gmx-users] Constraining hydrogen - heavy atom bonds with different naming.

Dear Gromacs Experts, I am pretty sure I have already answered this question long time ago but I cannot find it. What I did is I added a new residue for my system and it contains hydrogen atoms. Now, the thing is that all atoms names start with "M", so I have MH21, MH22, MCA1, etc. atoms. I want

Re: [gmx-users] index file after MD for non bonded interactions

On 3/1/16 4:27 AM, Nikhil Maroli wrote: Dear all, i have generated cyclic peptide nanotube in Lipid bilayer system and input files for GROMACS from charmm-gui . 50 ns MD is performed and i would like to study non bonded interactions, when i invoke gmx energy- i got 50 options ,but none of

Re: [gmx-users] Deuterium order parameter for POPC/POPS mixed lipid bilayer

On 3/1/16 1:20 AM, kamakshi sikka wrote: Hello everyone, I want to calculate deuterium order parameter for 25POPC/103POPS mixed lipid bilayer. But, I don't know how to make index groups for sn1 and sn2 acyl chains for both POPS and POPC lipids separately. Please help. Select by residue

Re: [gmx-users] grompp protein-ligand complex simulation

On 3/1/16 5:06 AM, Adamu, Aliyu wrote: Hi all, I am trying to run protein-ligand complex MD in Gromacs 4.6.7. Using opls-aa forcefield. I parameterised my ligand using topolbuild. I managed to defined the unit cell and added solvent successfully. But when trying to run grompp command for

Re: [gmx-users] Is simulated annealing mdp ok

On 3/1/16 5:30 AM, Mijiddorj Batsaikhan wrote: Dear gmx users, I would like to explore two proteins interactions in water using simulated annealing. in my topology file, my proteins are named Protein and Protein2. I have following 2 hesitations: 1. How to set energy groups in mdp file? I

Re: [gmx-users] adding mdp to amber99sb

On 3/1/16 1:14 PM, Irem Altan wrote: Hi, I am trying to add MPD to the amber99sb forcefields. I have added the necessary things to aminoacids.rtp, aminoacids.hdp, and atomtypes.atp, but when I run pdb2gmx I get the following error: Fatal error: Atom type H11 (residue MPD) not found in

[gmx-users] adding mdp to amber99sb

Hi, I am trying to add MPD to the amber99sb forcefields. I have added the necessary things to aminoacids.rtp, aminoacids.hdp, and atomtypes.atp, but when I run pdb2gmx I get the following error: Fatal error: Atom type H11 (residue MPD) not found in atomtype database I’m a bit confused, as I’d

[gmx-users] Is simulated annealing mdp ok

Dear gmx users, I would like to explore two proteins interactions in water using simulated annealing. in my topology file, my proteins are named Protein and Protein2. I have following 2 hesitations: 1. How to set energy groups in mdp file? I wrote "define = Protein Non-Protein" 2. Is mdp

Re: [gmx-users] generating martini-version of lipids

Hi Tsjerk I have created a "dppg.charmm36.map" file using the template provided by popg and dppc mapping . Then I had put 'dppg.charmm36,map' file in the Mapping folder. However, If I want to do forward transformation i.e. going from charmm36 to martini , issuing the following command, it

[gmx-users] grompp protein-ligand complex simulation

Hi all, I am trying to run protein-ligand complex MD in Gromacs 4.6.7. Using opls-aa forcefield. I parameterised my ligand using topolbuild. I managed to defined the unit cell and added solvent successfully. But when trying to run grompp command for addition of ion, I received fatal error: "

[gmx-users] index file after MD for non bonded interactions

Dear all, i have generated cyclic peptide nanotube in Lipid bilayer system and input files for GROMACS from charmm-gui . 50 ns MD is performed and i would like to study non bonded interactions, when i invoke gmx energy- i got 50 options ,but none of them contain option such as

Re: [gmx-users] generating martini-version of lipids

Hi Jagannath, Have a look at the mappings for dppc and popg. It's quite easy to create the one for popg. If you only want to do forward mapping it is sufficient to list one corresponding CG bead for each atom. Cheers, Tsjerk On Mar 1, 2016 07:41, "jagannath mondal" wrote: