Re: [gmx-users] Generating topology of 3b68.ent

Look for any "MISSING ATOMS" in the pdb file (in the REMARKS). Look at the coordinates given for the LYS in question and check if there are coordinates for the CG. Experimental data isn't "perfect." PDB entries have missing residues and missing atoms all the time because they couldn't be

Re: [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT

Hi, On Thu, Jan 7, 2016 at 11:30 AM Hubert Santuz wrote: > Hi Mark, > > You were right, MPT defines a constant UNDEFINED in their mpi++.h Why it > should not do? > Because if everybody wrote libraries like that, then nobody could use any generic-sounding name for a

Re: [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach

Hii Justin.. Since I am using PME option in my both simulation (Bound as well as alone), I think that it is necessary to use rerun option brfore parsing the values to g_lie. When I am running mdrun with new .mdp settings without PME option I am getting series of warnings and therefore program

Re: [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT

Hi, No, I don't have access to the MPT documentation, so you should start there. I would be pretty sure it wouldn't be faster, either ;-) Mark On Thu, 7 Jan 2016 13:25 Hubert Santuz wrote: > Hi, > > 2016-01-07 11:48 GMT+01:00 Mark Abraham : >

Re: [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach

On 1/7/16 5:54 AM, shagun krishna wrote: Hii Justin.. Since I am using PME option in my both simulation (Bound as well as alone), I think that it is necessary to use rerun option brfore parsing the values to g_lie. When I am running mdrun with new .mdp settings without PME option I am getting

Re: [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT

Hi, 2016-01-07 11:48 GMT+01:00 Mark Abraham : > Hi, > > On Thu, Jan 7, 2016 at 11:30 AM Hubert Santuz > wrote: > > > Hi Mark, > > > > You were right, MPT defines a constant UNDEFINED in their mpi++.h Why it > > should not do? > > > > Because if

Re: [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT

Finally, I found a solution by digging on MPT C++ bindings. In fact, at the end of the MPT mpi.h file, we have: if !defined(MPI_NO_CPPBIND) #include "mpi++.h" #endif So MPT expose the C++ bindings by default. To prevent that, I add the macro to src/gromacs/utility/gmxmpi.h : /* MPI C++ binding

[gmx-users] How to get a compressed pull force output from SMD simulation ?

Dear Users, I use GROMACS to do SMD simulation. I have the pullf.xvg file , but it is very large. I also have the smd.xtc file. I have used it to calculate the COM separation distance between the two pulled groups. I want to plot force vs COM separation. Can I calculate the pull force from the

[gmx-users] Error while running mdrun with rerun option for LIE calculation

Hiii Justin, Thank you very much for your help. After changing my settings according to your suggestions I am not getting the previous errors. :) The grompp command ran successfully, but when I am evoking the mdrun using rerun option I am getting a fatal error. Please have a look at my terminal

[gmx-users] preapration of non-standard residue

Dear Gromacs Users, I'd like to prepare my system for MD simulations. I have non-standard residue. I prepared a topology and coordinates by antechamber. I know, I should add it to itp file. But what exactly I should do? Thank you in advance, Marta -- Gromacs Users mailing list * Please search

[gmx-users] Visualization of conf.gro and confout.gro

Dear Gromacs Users, I did NPT simulations with a system containing 15000 atoms of polymers. Initially, conf.gro was visualized in VMD and showed all connections are OK. However, the confout.gro (final output configuration) seems to look bad. Some of bonds are disconnected at the outer surface

[gmx-users] Generating topology of 3b68.ent

Good evening everyone, I was trying to generate the topology of the ligand binding domain of the human androgen receptor (3B68) with pdb2gmx using pdb2gmx -f 3b68.ent -o ar.gro -p ar.top -ignh using the AMBER-ILDN ff and implict solvent (therefore typing 6 and 6 again on gromacs v. 4.6.5) and it

Re: [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT

Great. Thanks. Hubert 2016-01-07 18:33 GMT+01:00 Mark Abraham : > Hi, > > Thanks, I have now proposed that fix at https://gerrit.gromacs.org/5535. > If > accepted, it'll be in GROMACS 5.1.2 > > Mark > > On Thu, Jan 7, 2016 at 6:05 PM Hubert Santuz

Re: [gmx-users] Generating topology of 3b68.ent

Hi, It could just be missing from the experimental data. You'll need to do some detective work about that pdb entry. Mark On Thu, 7 Jan 2016 19:05 Simone Bolognini wrote: > Good evening everyone, > I was trying to generate the topology of the ligand binding domain of

[gmx-users] Correct method to do Cartesian PCA

Hi All, I am trying to reproduce the Cartesian PCA results for ALA3 in water by Altis et al. (Fig.2 of Dihedral angle principal component analysis of molecular dynamics simulations. http://dx.doi.org/10.1063/1.2746330 ) It is probably the most well-known PCA analysis results. I created a system

Re: [gmx-users] Correct method to do Cartesian PCA

Hi Bin, The procedure is correct, provided you ensured that the input trajectory did not have PBC jumps. But the paper you refer to is on dihedral angle PCA... Cheers, Tsjerk On Jan 7, 2016 23:06, "Bin Liu" wrote: > Hi All, > > I am trying to reproduce the Cartesian