Re: [gmx-users] Enthalpy of Vaporization

On 10/5/15 1:50 PM, Pallavi Banerjee wrote: Correct me if I am wrong, please. Ugas would be obtained from a simulation of a single molecule in vacuum. And U liq would be the total potential energy of the system (which is given by g_energy) minus the total bonded potential energy

Re: [gmx-users] Enthalpy of Vaporization

Correct me if I am wrong, please. Ugas would be obtained from a simulation of a single molecule in vacuum. And U liq would be the total potential energy of the system (which is given by g_energy) minus the total bonded potential energy (bonds+angles+dihedrals). Am I thinking right? Thanks.

Re: [gmx-users] Building gromacs on CRAY XC40

On Mon, Oct 5, 2015 at 5:52 PM, Mark Abraham wrote: > Hi, > > Indeed, although having the craype-ivybridge module loaded (when perhaps it > was not loaded at CMake time) does not look like it would help. > That certainly does not look right (either), if the target is

Re: [gmx-users] Enthalpy of Vaporization

On 10/5/15 2:01 PM, Rasoul Nasiri wrote: On Mon, Oct 5, 2015 at 6:52 PM, Justin Lemkul wrote: On 10/5/15 1:50 PM, Pallavi Banerjee wrote: Correct me if I am wrong, please. Ugas would be obtained from a simulation of a single molecule in vacuum. And U liq would be the

Re: [gmx-users] Enthalpy of Vaporization

On Mon, Oct 5, 2015 at 7:03 PM, Justin Lemkul wrote: > > > On 10/5/15 2:01 PM, Rasoul Nasiri wrote: > >> On Mon, Oct 5, 2015 at 6:52 PM, Justin Lemkul wrote: >> >> >>> >>> On 10/5/15 1:50 PM, Pallavi Banerjee wrote: >>> >>> Correct me if I am wrong, please.

[gmx-users] RMSF calculation of carbon alpha

Hi there, I want to calculate ht RMSF of the carbon alpha. First which atoms are used if I calculate the RMSF per residue with -res and how can I calculate the RMSF of carbon alpha or NH vector etc? Can’t seem to find an input except for the group of the alignment for the -fit Thank you,

[gmx-users] (no subject)

GROMACS users, I was trying to perform a MD simulation of a system with a protein with Ag+ metal ion but realized that GROMACS does not have parameters for the Ag+ ion. I tried to include the parameters in the ion.itp file but did not succeed yet. Does anyone knows the right procedure to

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi, Sorry for the confusion. Now I have generated a small xtc file and a very big pdb file. I can able to access small xtc file but unable to read the large pdb file (~10GB) (terminating with the same error as reported earlier). Does it mean my installation has some problem? On Mon, Oct 5, 2015

Re: [gmx-users] Gromacs

GROMACS users, I was trying to perform a MD simulation of a system with a protein with Ag+ metal ion but realized that GROMACS does not have parameters for the Ag+ ion. I tried to include the parameters in the ion.itp file but did not succeed yet. Does anyone knows the right procedure to

Re: [gmx-users] RMSF calculation of carbon alpha

Hi Ebert, Use C-alpha as the group. Yes, it will be used for fitting and calculation of the RMSF. Cheers, Tsjerk On Oct 5, 2015 22:44, "Ebert Maximilian" wrote: > Oh infact no thats not the case it is still the RMSF of all atoms in the > residue. So back to my initial

Re: [gmx-users] RMSF calculation of carbon alpha

Oh infact no thats not the case it is still the RMSF of all atoms in the residue. So back to my initial question. How can I calculate the RMSF on the Ca of each residue? Sorry if this caused any confusion. Max > On Oct 5, 2015, at 4:36 PM, Ebert Maximilian wrote: > > I

Re: [gmx-users] Pull Code Error "unknown left hand"

Hi, take a look at the mdout.mdp grompp output file. There you should see how the pull-related parameters are called in the version you were using. Maybe you just need to use minus signs instead of the underlines. Best, Carsten > On 05 Oct 2015, at 04:25, Stella Nickerson

[gmx-users] PBC

Dear users, If I dont define pbc=no, what is the default type for gromacs? Is it right if I dont use pbc=no in my system while using grid for ns-type? thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] error unknown bond_atomtype CH1

After grompp command i got this error Fatal error unknown bond_atomtype CH1 Please help me solve his error thanks in advance Surbhi -- 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

Re: [gmx-users] error unknown bond_atomtype CH1

Hi Surbhi, You are getting this error due to the Atomtype CH1 is not defined in your forcefield. Try to see if the CH1 is defined in atomtype.atp as well as ffbonded.itp On Mon, Oct 5, 2015 at 1:20 PM, surbhi mahajan wrote: > After grompp command i got this

[gmx-users] genion problem

Dear all I want to use bromide for neutralize my system. I wrote genion -s ions.tpr -c file.gro -p topol.top -pname K -nname BR -nn 24. After I cheked it the gromacs read Boron intead of bromide. I wrote command -nname BR -nn 24. and I did not use K but in all cases my output was boron and I did

Re: [gmx-users] h-bonds by g_hbond and VMD and ptraj

Hi Erik, Thank you for fast reply. I knew about differences between definitions of angle criterion in Gromacs, VMD and cpptraj but I didn't realize that there is nontrivial relationship between these two different definitions. I have gone deeper into this problem and now it makes sence to me.

[gmx-users] coarse grained multi-body cut-off distance error

Dear Gromacs user, The coarse grained simulation was done by using the files prepared by the SMOG server. However, i got an error as follows: Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: LJ-14 of

[gmx-users] Energy minimization error

Thank you for your great help on specbond.dat file. I defined it and I could go ahead until Energy minimization step. I have used this minim.mdp file ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep

[gmx-users] installing gromacs-5.0.5

Hello everybody; I want to install gromacs-5.0.5 in ubuntu-14.04 using the installation instruction in the website "gromacs.org", but in the "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON" line I got this error: -- No compatible CUDA toolkit found (v4.0+), disabling native GPU

Re: [gmx-users] RMSF calculation of carbon alpha

Thanks for the clarification Tsjerk. So my previous assumption was right. Basically if I want to align on the backbone but want the RMSF of Calpha I need to align first, save the trajectory and do RMSF with -nofit right? Max > On Oct 5, 2015, at 4:54 PM, Tsjerk Wassenaar

Re: [gmx-users] RMSF calculation of carbon alpha

I think I can answer my own question again. The group you use for root mean square calculation is also the RMSF group. If the group has more than one atom per residue and I use -res I get the average RMSF of all atoms per residue. Hope this is correct. Max > On Oct 5, 2015, at 2:46 PM, Ebert

Re: [gmx-users] Free Energy of Liquid Water

Thank you, Professor Farais de Moura. That method of integrating to an ideal gas makes sense. However, I'm having trouble figuring out how to deal with the temperature. I hope my question isn't too basic, but I can't find any examples online and I know I am misunderstanding how it works. I want

Re: [gmx-users] Enthalpy of Vaporization

My system is one molecule of Propanamide. I need to see if my force field makes the molecule water soluble or not, for which I would need its cohesive energy, and this in turn would require the heat of vaporization. So, I should include the total potential energy for both gas and liquid phase in

[gmx-users] Hydrogen virtual sites and AMBER FF

IIRC, Mark Abraham wrote that there are some issues with implementation of vsites with amber ffs in GROMACS. Any more details? Is it possible to use amber99sb-ildn with -vsite option to speed up calculation? -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] PBC

Hi, I don't really remember. I suspect not, so I would look up the docs for ns-type, which should mention limitations, and otherwise try it out. grompp and/or mdrun are pretty good at complaining about things they can't do. Mark On Mon, Oct 5, 2015 at 12:56 PM mah maz

Re: [gmx-users] Building gromacs on CRAY XC40

Hi, Often the XC40 has a different kind of login vs compute node. Here it looks like you have configured for the compute node, but are actually using a toolchain to build for the login node. Use the Cray MPI wrapper compiler configured to use gcc as its back end as the compiler to give to CMake,

Re: [gmx-users] Energy minimization error

Hi, Look at atom 380 and see why the forces might be high. Mark On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani wrote: > Thank you for your great help on specbond.dat file. I defined it and I > could go ahead until Energy minimization step. I have used this

Re: [gmx-users] PBC

Hi Mark, Thanks. It seems the default is pbc =xyz. But my question is if I don't use PBC, can I use grid, or grid is only meaningful when PBC is defined? On Mon, Oct 5, 2015 at 11:07 AM, mah maz wrote: > Dear users, > > If I dont define pbc=no, what is the default type for

Re: [gmx-users] PBC

Hi, See top of http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html regarding defaults. Or you can leave it blank and inspect what gmx grompp writes to the mdout.mdp. Whether any PBC setting makes sense depends what you're trying to do, which we don't know. Mark On Mon, Oct

Re: [gmx-users] Pull Code Error "unknown left hand"

Hi, Things change between versions when we recognize limitations of old decisions. 5.0 certainly recognizes pull-ngroups, so I think you were using a non-matching grompp at some point. You do have the option of reading the .mdp documentation for the version you're using. :-) (Of course, if it's

Re: [gmx-users] genion problem

On 10/5/15 2:26 AM, Golnaz Roudsari wrote: Dear all I want to use bromide for neutralize my system. I wrote genion -s ions.tpr -c file.gro -p topol.top -pname K -nname BR -nn 24. After I cheked it the gromacs read Boron intead of bromide. I wrote command -nname BR -nn 24. and I did not use K

Re: [gmx-users] Hydrogen virtual sites and AMBER FF

Hi, On Mon, Oct 5, 2015 at 12:49 PM Timofey Tyugashev wrote: > IIRC, Mark Abraham wrote that there are some issues with implementation > of vsites with amber ffs in GROMACS. > Shrug, that's meaningless without context. > Any more details? Is it possible to use

[gmx-users] Enthalpy of Vaporization

Hello Users, I need to calculate the cohesive energy for my system, for which the enthalpy of vaporization is needed. Am I right to assume that just the non-bonded interaction energy (potential energy) is required to calculate the enthalpy of vaporization ? Many Thanks! -Pallavi Banerjee --

Re: [gmx-users] Enthalpy of Vaporization

On 10/5/15 10:53 AM, Pallavi Banerjee wrote: Hello Users, I need to calculate the cohesive energy for my system, for which the enthalpy of vaporization is needed. Am I right to assume that just the non-bonded interaction energy (potential energy) is required to calculate the enthalpy of

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi, That unfortunately doesn't tell us anything, since 1.5GB can still be read with 32-bit file operations. You didn't answer any of the questions: can you open very small xtc files, or very large (requiring 64-bit access) gro/pdb files, or not? We are still thinking that you should be able to

Re: [gmx-users] Install Gromacs on VirtualBox

Oh, that was easy, should have asked about what the value of "GMX_SIMD" is in the CMake cache. Given that the GROMACS build system enabled AVX2 SIMD on your VM which seems to not support anything above SSE2, it's not a surprise that the first math instruction crashes the run. Immediate solution:

Re: [gmx-users] Building gromacs on CRAY XC40

Hi, Indeed, although having the craype-ivybridge module loaded (when perhaps it was not loaded at CMake time) does not look like it would help. Mark On Mon, Oct 5, 2015 at 5:47 PM Szilárd Páll wrote: > On Mon, Oct 5, 2015 at 6:15 AM, kevin chen

Re: [gmx-users] Building gromacs on CRAY XC40

On Mon, Oct 5, 2015 at 6:15 AM, kevin chen wrote: > Dear Gromacs users, > > I am trying to build gromacs on our latest supercomputer CRAY XC40, but the > following errors using gcc and fftw. Here's my list of module loaded and > install script, can anyone give any

Re: [gmx-users] Enthalpy of Vaporization

This non-zero value becomes quite significant if you are dealing with highly flexible molecules - Internal molecular dynamics effects are different in the gas and liquid phases. Rasoul On Mon, Oct 5, 2015 at 3:53 PM, Pallavi Banerjee < pallavis...@students.iiserpune.ac.in> wrote: > Hello