Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

Thanks for the advice I will do this exercise with other molecule and will let you know the results. but, why i was confused is because in one PMF curve all the free energy values are on the positive side where as the other has all free energy values on the negative side. do these signs are not

Re: [gmx-users] append simulation

On 5/4/15 7:54 PM, Nilesh Dhumal wrote: On 5/4/15 6:08 PM, Nilesh Dhumal wrote: Hello Gromacs Users, I have finished 30ns simulation and I want to run 30ns more. If I use append yes, will it append to existing trajectory file. Will I get the final 60 ns trajectory. Well, that's the exact

Re: [gmx-users] append simulation

> > > On 5/4/15 6:08 PM, Nilesh Dhumal wrote: >> Hello Gromacs Users, >> >> I have finished 30ns simulation and I want to run 30ns more. >> If I use append yes, will it append to existing trajectory file. >> Will I get the final 60 ns trajectory. >> > > Well, that's the exact purpose of the -append

Re: [gmx-users] append simulation

On 5/4/15 6:08 PM, Nilesh Dhumal wrote: Hello Gromacs Users, I have finished 30ns simulation and I want to run 30ns more. If I use append yes, will it append to existing trajectory file. Will I get the final 60 ns trajectory. Well, that's the exact purpose of the -append option does, so yes

[gmx-users] append simulation

Hello Gromacs Users, I have finished 30ns simulation and I want to run 30ns more. If I use append yes, will it append to existing trajectory file. Will I get the final 60 ns trajectory. Nilesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_

Re: [gmx-users] CHARMM36 Termini Topology Incomplete

On 5/4/15 5:43 PM, João Rodrigues wrote: Hi Justin, In order to solve the issue, I need to know exactly what you're doing - exact command and full pdb2gmx screen output, please. Issues with missing parameters for neutral termini should have been fixed well over a year ago; you are using the

Re: [gmx-users] CHARMM36 Termini Topology Incomplete

Hi Justin, In order to solve the issue, I need to know exactly what you're doing - > exact > command and full pdb2gmx screen output, please. Issues with missing > parameters > for neutral termini should have been fixed well over a year ago; you are > using > the latest ports, correct? I released

Re: [gmx-users] CHARMM36 Termini Topology Incomplete

On 5/4/15 4:09 PM, Jarrett Lee Wise wrote: I had similar problems when I was making polymers. You have to input those parameters directly or delete those lines in the itp/topology file depending if they are important or not. The correct way would be to do quantum I don't know how one decide

Re: [gmx-users] CHARMM36 Termini Topology Incomplete

On 5/4/15 3:43 PM, João Rodrigues wrote: Hi all, I am trying to setup a simulation of a peptide with neutral termini, using the CHARMM36 port from the MacKerell lab. While pdb2gmx works well, grompp fails with several erros about missing parameters, e.g.: ERROR 1 [file topol.top, line 1225]:

Re: [gmx-users] CHARMM36 Termini Topology Incomplete

I had similar problems when I was making polymers. You have to input those parameters directly or delete those lines in the itp/topology file depending if they are important or not. The correct way would be to do quantum calculations for the missing parameters, but I inserted similar ones for

[gmx-users] CHARMM36 Termini Topology Incomplete

Hi all, I am trying to setup a simulation of a peptide with neutral termini, using the CHARMM36 port from the MacKerell lab. While pdb2gmx works well, grompp fails with several erros about missing parameters, e.g.: ERROR 1 [file topol.top, line 1225]: No default U-B types ... ERROR 4 [file to

Re: [gmx-users] Grompp error "No default Ryckaert-Bell. types"

True, thats why i mentioned Mark.:-) In all honesty, though, for small molecules, i would prefer to ignore the new format and actually add everything in the rtp entry to make ffbonded look like less of a zoo. Also, it was late night of extreme gromacs intercourse for me, which finally paid off. :-

Re: [gmx-users] Grompp error "No default Ryckaert-Bell. types"

On 5/4/15 1:06 PM, Alex wrote: JL> 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are JL> required to define connectivity. Remaining bonded interactions are then deduced JL> from bond connectivity. If a directive like [angles] or [dihedrals] is present, JL> those

Re: [gmx-users] Grompp error "No default Ryckaert-Bell. types"

JL> 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are JL> required to define connectivity. Remaining bonded interactions are then deduced JL> from bond connectivity. If a directive like [angles] or [dihedrals] is present, JL> those values are used, instead. If an [a

Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

Can you walk me through that image and tell me what you see that is different from what you expect? I see a maximum at z=0 in both cases (I presume z=0 is the bilayer center). I'm happy to continue guessing, but you are really best to take something like hexane in a simplified bilayer and do a t

Re: [gmx-users] Justin biphasic tutorial with controlled adsoption of protein

On 5/3/15 10:29 PM, James Lord wrote: Hi Justin, I definitely saw this in the manual but as I said before couldn't get the part "a suitable [position_restraints] " and "negative force constant" in your earlier email. Would you please let me know the right way of doing this? may be an example of

Re: [gmx-users] atom freezing during simulation

On 5/4/15 1:10 AM, mah maz wrote: Hi Justin, Unfortunately, I am looking at the right atoms! Coordinates of the frozen atoms are different from their initial ones and they have non-zero velocities. I set up the .mdp file as follows: freezegrps = frz1 frz2 freezdim = x y z x y z Is it the corre

Re: [gmx-users] Grompp error "No default Ryckaert-Bell. types"

On 5/4/15 4:20 AM, Alex wrote: The rtp file format and its acceptable entries are not forcefield-specific (oplsaa seems to look up triplets for [ angles ] elsewhere), I just wanted to give an example of that. The oplsaa version of aminoacids.rtp only lists dihedral and improper angles explicit

Re: [gmx-users] Grompp error "No default Ryckaert-Bell. types"

The rtp file format and its acceptable entries are not forcefield-specific (oplsaa seems to look up triplets for [ angles ] elsewhere), I just wanted to give an example of that. The oplsaa version of aminoacids.rtp only lists dihedral and improper angles explicitly, and that is exactly what's g

Re: [gmx-users] Grompp error "No default Ryckaert-Bell. types"

"Which angles?" -- wait until Mark Abraham gets here. You must have a very special version of aminoacids.rtp Example: https://github.com/gromacs/gromacs/blob/master/share/top/gromos43a2.ff/aminoacids.rtp > Thank you But which angles I need to add in .rtp file. are you talking about im

Re: [gmx-users] Grompp error "No default Ryckaert-Bell. types"

You said you found the rtp entry to be correct, and yet the one you attached has no angles listed, none whatsoever.  Alex > Thank you for your reply. I am simulating a PLGA (poly lactic co-glycolic acid molecle). I get the topology file and I solvated the molecule.  my system is neutra