Re: [gmx-users] How to examine our created topology

Dear Justin, I simulate 2,6 dimethylpyridine (lutidine), C7H9N. I use ''gromos43a1'' force field, and I have taken the charges on atoms from Gaussian software. By manipulating charges on the atoms I can get better agreement with experiment for the bulk, but then I loose it's aqueous properties

Re: [gmx-users] Peptide-membrane simulation force field parameters

Thanks Justin for the reply and suggestions. I have more of less similar functional groups as that of the amino acid side chains. Yes, I have figured out some chemical analogy to parametrize the residues. Tarak On Wed, Feb 4, 2015 at 6:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/4/15

Re: [gmx-users] Umbrella sampling restraining potential

On 2/14/15 7:56 PM, Agnivo Gosai wrote: Dear Users The PMF generated by umbrella sampling of my system appears to be converged and the calculated free energy of binding is close to that in published literature. I believe a necessary check for the convergence is the overlap and smoothness of

Re: [gmx-users] error: Atom 1 in multiple Energy Mon. groups

thank you so I have to run different times !? On Sun, Feb 15, 2015 at 5:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/15/15 9:12 AM, nazli kashani javid wrote: Thank you very much. what do you mean of multiple energy evaluations ? do you mean I should change my .mdp file like

Re: [gmx-users] error: Atom 1 in multiple Energy Mon. groups

thanks, that's very kind of you. On Sun, Feb 15, 2015 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/15/15 9:29 AM, nazli kashani javid wrote: thank you so I have to run different times !? For any given simulation, you just use mdrun -rerun as many times as needed, with

[gmx-users] lower Area per lipid for DPPC with CHARMM36

Dear All, All atom simulation of DPPC bilayer (128 lipids) is resulting a low area per lipid (sliding down from ~58 to ~54 in 4 ns NPT). I'm performing the simulation in gromacs-5.0.4 with the charmm36 force field parameters for the lipid molecules. The NPT.mdp is pasted bellow,

[gmx-users] error: Atom 1 in multiple Energy Mon. groups

Hi all I want to calculate interaction energy of my protein that includes 4 individual chains(a,b,c and d). at first I define an index file. It contains: [ chaina ] 1234 ...454 [ chainb ] 455 456 457 ...919 [ chainc ] 920 921 922 1373 [ chaind ] 1374 1375 1376 1838 [

Re: [gmx-users] lower Area per lipid for DPPC with CHARMM36

On 2/15/15 7:39 AM, tarak karmakar wrote: Dear All, All atom simulation of DPPC bilayer (128 lipids) is resulting a low area per lipid (sliding down from ~58 to ~54 in 4 ns NPT). I'm performing the simulation in gromacs-5.0.4 with the charmm36 force field parameters for the lipid molecules.

Re: [gmx-users] error: Atom 1 in multiple Energy Mon. groups

On 2/15/15 9:29 AM, nazli kashani javid wrote: thank you so I have to run different times !? For any given simulation, you just use mdrun -rerun as many times as needed, with whatever groups are of interest. Interaction energies are just post-processing measures, really. They can be

Re: [gmx-users] How to examine our created topology

On 2/15/15 9:39 AM, Faezeh Pousaneh wrote: Dear Justin, I simulate 2,6 dimethylpyridine (lutidine), C7H9N. I use ''gromos43a1'' force field, and I have taken the charges on atoms from Gaussian software. By manipulating charges on the atoms I can get better agreement with experiment for the

Re: [gmx-users] Semiisotropic pressure coupling

Dear Justin, I have sent the files to you at your vt.edu Thanks, sxn On Sun, Feb 15, 2015 at 7:59 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/14/15 9:52 PM, shivangi nangia wrote: Hello Justin, I ran the simulation for 100 ns and I still get low APL at 303 K, 0.58 nm^2 :(

Re: [gmx-users] Semiisotropic pressure coupling

On 2/15/15 11:32 AM, shivangi nangia wrote: Sorry about that. Here it is: https://drive.google.com/file/d/0B9SJqGLyLrwVcThWbEthaFo3SGc/view?usp=sharing So this is actually a system in which a peptide is peripherally bound to a POPC membrane. That complicates things significantly. Not

[gmx-users] NVT step

Dear Justin,I studied your toturial (KALP15 in DPPC).I'm simulating a drug at dppc, at nvt step i used this command: mdrun -deffnm nvt -v , but i gave this error:  Fatal error: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off outof the domain decomposition cell of

Re: [gmx-users] electric fields

Hi all, I need to apply magnetic and also alternating electric field to my system, but I can't find any options. Can anyone help me? thanks! On Fri, Feb 13, 2015 at 8:44 PM, mah maz mahma...@gmail.com wrote: Dear all, What kinds of electric and magnetic fields are available in gromacs? Are

Re: [gmx-users] electric fields

On 2/15/15 12:31 PM, mah maz wrote: Hi all, I need to apply magnetic and also alternating electric field to my system, but I can't find any options. Can anyone help me? Probably because those options don't exist. Constant electric fields are described in manual section 7.3.26 (conveniently

Re: [gmx-users] Semiisotropic pressure coupling

On 2/15/15 1:02 PM, shivangi nangia wrote: Dear Justin, Thanks for the continuous help. Since I have done reverse CG, The CG POPC was equilibrated alone anisotropically, The APL was fine there. On reverse CG and NVT its still fine, it only after NPT it starts dropping. Of course it's fine

Re: [gmx-users] Can only find GPU'S on first node

Have you tried using: mpirun -np (number of mpi-processes total) -npernode (number of gpus per node) . when you execute mdrun? Not sure if it will do the trick, but it looks like it may work. What that command should do it limit the number of mpi-process to the number of gpus (so that

Re: [gmx-users] electric fields

Dear Justin, David Thank you for your reply. I have also seen not implemented yet as Justin said. David, I hope your option E-xt works. But still I don't know if I should supply its parameters the same as E-x or it would be different. Thanks a lot! On Sun, Feb 15, 2015 at 9:01 PM, mah maz

Re: [gmx-users] electric fields

On 2015-02-15 20:49, mah maz wrote: Dear Justin, David Thank you for your reply. I have also seen not implemented yet as Justin said. David, I hope your option E-xt works. But still I don't know if I should supply its parameters the same as E-x or it would be different. The field has the form

Re: [gmx-users] electric fields

On 2015-02-15 18:35, Justin Lemkul wrote: On 2/15/15 12:31 PM, mah maz wrote: Hi all, I need to apply magnetic and also alternating electric field to my system, but I can't find any options. Can anyone help me? Probably because those options don't exist. Constant electric fields are

Re: [gmx-users] electric fields

On 2/15/15 1:56 PM, David van der Spoel wrote: On 2015-02-15 18:35, Justin Lemkul wrote: On 2/15/15 12:31 PM, mah maz wrote: Hi all, I need to apply magnetic and also alternating electric field to my system, but I can't find any options. Can anyone help me? Probably because those options

Re: [gmx-users] NVT step

On 2/15/15 12:44 PM, asasa qsqs wrote: Dear Justin,I studied your toturial (KALP15 in DPPC).I'm simulating a drug at dppc, at nvt step i used this command: mdrun -deffnm nvt -v , but i gave this error: Fatal error: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off

Re: [gmx-users] counting dihedral transitions not working with gmx angle (Mark Abraham)

Hi, As far as I can see, that should work... Looks like a bug, but I can't see why. If you can reproduce it with a small piece of your trajectory, please make a tarball of the input files and file an issue at http://redmine.gromacs.org and I'll take a look. Thanks, Mark On Feb 13, 2015 4:51 PM,

[gmx-users] Re;calculating interaction energies of dimers and ligand

Dear Justin, I notice that -rerun option in mdrun. As per your suggestion, i have made a tpr file using energyrps in md.mdp file as like this gmx grompp -f md.mdp -c npt.gro -t npt.cpt -o check.tpr and tried to use mdrun -reun gmx mdrun -rerun check but end up with Can not

[gmx-users] Regarding DSSP

Hello all: I am not really sure, what are the various compatibility issues between the do_dssp program of different Gromacs versions and the versions of the DSSP program itself. I am trying to use dssp 2.0.4 and Gromacs 4.5.6. I have used export DSSP=/usr/bin/dssp and then do_dssp - I am

[gmx-users] Plz help File input/output error: Cannot write trajectory frame;

Hi I am encountering this error for the second time. The simulation exactly stops at 9 NS with this message. Earlier I have the same problem and now I am have check the disk space and there is around 120 GB free space. Is this could be the system hardware is not compatible or its just the hard

Re: [gmx-users] Problem executing do_dssp in gromacs

Hi Justin, Yes, I have checked the env variables and file is also executable. But still giving fatal error and asking me to specify the dssp version. Aarti On Fri, Feb 13, 2015 at 8:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/13/15 4:41 AM, Aarti rana wrote: Hi, I am new to

[gmx-users] Re;calculating interaction energies of dimers and ligand

Dear Justin, I already ran 10 ns without mentioned the energyrps. Now I have added the energyrps in md.mdp file. Should i need to rerun 10 ns again to get the interaction energies? what does mdrun -rerun ? On 2/13/15 7:07 AM, RJ wrote: Dear all, I need to calculate the interaction