Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

On 4/28/12 12:28 PM, J B wrote: Hi, the distance is 3.89 nm and the z-dimension is roughly 8 nm Is the problem specific to cylinder geometry? Do other settings work? Does it make a difference if you set values for pull_r0 and pull_r1? -Justin > Date: Sat, 28 Apr 2012 09:18:31 -040

Re: [gmx-users] Make an index file

On 4/28/12 2:06 PM, Peter C. Lai wrote: #2 Generally a good idea to keep the names consistent, however - why are you using POP in the coordinate file instead of POPC? If it is a .pdb file, the standard residue name occupies 3 characters. Many files (including those from Tieleman) are distr

Re: [gmx-users] Make an index file

#2 Generally a good idea to keep the names consistent, however - why are you using POP in the coordinate file instead of POPC? -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Shima Arasteh wrote: Dear gmx users, I want to simulate POPC in water. In equilibration step,

[gmx-users] Make an index file

Dear gmx users, I want to simulate POPC in water. In equilibration step, I have to make an index file. But when I enter this command, I do not know to choose which group to make a suitable .ndx file which matches the molecule types and molecules sections in .top file . The .top file contains t

Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

oops I meant /usr/local/gromacs/bin in PATH also 4.5.4 has support for threading if compiled that way...Most clusters don't use it because nodes on separate chassis usually don't support shared memory with each other. We get really bad performance when using threading-over-scalemp as compared t

Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

possibly. Make sure PATH includes /usr/local/bin and LD_LIBRARY_PATH includes the path where libmd_mpi.so and libgmx_mpi.so are located. try using mdrun -v and > somelogfile after the mpirun line (like mpirun blah -np 8 mdrun -v -deffnm etcetc > mpilog). the contents of mpilog will tell you wha

[gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun

Hi, Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you know, automatic threading is awesome because it allows me to start parallel runs without calling mpirun. So on version 4.5.5, I can start a job on eight CPUs using simply the command: mdrun -s topol.tpr -nt 8 However, n

RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

Hi, the distance is 3.89 nm and the z-dimension is roughly 8 nm > Date: Sat, 28 Apr 2012 09:18:31 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Umbrella sampling PMF, drug and membrane with > pull_geometry=cylinder > > > > On 4/28/12 5:12 AM, J B

Re: [gmx-users] Making Disulfide Bonds

On 4/28/12 10:25 AM, James Starlight wrote: Francesco, Thanks, I find your aproach very handfull :) Justin, in that example I've defined in minim.mdp This would have been useful to state up front. Your previous question implied that you didn't know if any special keywords were necessary

Re: [gmx-users] Making Disulfide Bonds

Francesco, Thanks, I find your aproach very handfull :) Justin, in that example I've defined in minim.mdp *disre = simple **disre_f = 5000 in the topology.top I've included * [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 1 10 10 10.18 0.20 0.22 1.0 w

Re: [gmx-users] Making Disulfide Bonds

On 4/28/12 10:08 AM, James Starlight wrote: .. and the main question- what should be in mdp file of such restrained minimisation ? Today I've done vry properly minimisation of such system in vacuum with the CG minimisator and applied disres ( above example ) with big force constant ( disres op

Re: [gmx-users] Making Disulfide Bonds

Hi James, usually I insert by hand a bond in the topology file between the two atoms and then I minimize. This bond doesn't cause the generataion of angles and dihedrals, butit is enough to make the atom closer. Francesco Il 28/04/2012 16:08, James Starlight ha scritto: .. and the main questi

Re: [gmx-users] Making Disulfide Bonds

.. and the main question- what should be in mdp file of such restrained minimisation ? Today I've done vry properly minimisation of such system in vacuum with the CG minimisator and applied disres ( above example ) with big force constant ( disres options have been defined in the minim.mdp file ).

Re: [gmx-users] blue gene running error

On 28/04/2012 4:14 PM, Albert wrote: hello Mar: thanks a lot for kind reply. From the link you you mentioned, it seems that this problem comes from the MD system itself. However, it goes well in my workstation. Moreover, I visualized and analyzed the results from my workstation running, ev

[gmx-users] simulation in vaccum

Hello Everyone, I am trying to pull ligand biotin out of the streptavidin protein.Following the tutorial Protein ligand complex by Justin ,i have done till energy minimization step skipping adding solvent and ion step,and skipping pressure and temperature equilibration.Now how to proceed further t

Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

On 4/28/12 5:12 AM, J B wrote: Hi. I am trying to the the PMF of transferring a drug molecule from the aqueous phase to a lipid bilayer. In order to minimize the effects of membrane undulations I tried to use pull_geometry=cylinder. Whenever I run a short simulation with umbrella sampling st

Re: [gmx-users] calculation of the mean B factor of a PDB file

On 4/28/12 5:41 AM, Acoot Brett wrote: Dear All, Will you please tell me a method or a server which can calculate the mean B factor of all residues in a PDB file? A simple script to parse out the B-factor field and calculate the average should do the trick. -Justin --

Re: [gmx-users] Making Disulfide Bonds

Hi Francesco! So I must define in the current topology the disres bettwen two S atoms ( in the below example 1 and 10 ) to apply hormonic restains [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 1 10 10 10.18 0.20 0.22 1.0 to restrain this atoms within 0.2 nm. Doe

Re: [gmx-users] Making Disulfide Bonds

Hi James, usually people run a minimization using distance restrain on the two atoms in order to make them closer. Then the obtained cnfiguration is used to recalculate the topology. Francesco 2012/4/28 James Starlight > Dear Gromacs Users! > > I have a model of my protein wich has 4 S-S bounds

[gmx-users] Making Disulfide Bonds

Dear Gromacs Users! I have a model of my protein wich has 4 S-S bounds in the loop regions. So I want to define in topology all those four S-S linkage. Unfortunatelly one of that S-S have not been recognised by Gromacs ( Also I've tried to check this bond in pymol and found that distance between

[gmx-users] calculation of the mean B factor of a PDB file

Dear All,   Will you please tell me a method or a server which can calculate the mean B factor of all residues in a PDB file?   Cheers,   Acoot   -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs

[gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

Hi. I am trying to the the PMF of transferring a drug molecule from the aqueous phase to a lipid bilayer. In order to minimize the effects of membrane undulations I tried to use pull_geometry=cylinder. Whenever I run a short simulation with umbrella sampling starting from a configuration with