Re: [gmx-users] backbone contact analysis of martini cg protein

can anyone please give me some idea. On 5/30/18, SHAHEE ISLAM wrote: > hi, > i want to calculate the contact between the backbone of protein(it is > a coarse grained protein using martini force field).how i will make > .ndx file to calculate the contact. > > thanking you > shahee islam >

[gmx-users] backbone contact analysis of martini cg protein

hi, i want to calculate the contact between the backbone of protein(it is a coarse grained protein using martini force field).how i will make .ndx file to calculate the contact. thanking you shahee islam university of calcutta -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Gromacs installation with GPU support in Windows 7

My bad, I missed a line in the warning message: Building NVCC (Device) object src/gromac/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/Release/libgromacs_generated_nbnxn_cuda.cu.obj CMake Warning (dev) at libgromacs_generated_nbnxn_cuda.cu.obj.Release.cmake:74: Syntax Warning in cmake code

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

Dear Micholas, I have many hydrocarbons (small to large) for study, C8 - C50, . -- 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 http://www.gromacs.org/Support/Mailing_Lists * For

Re: [gmx-users] Gromacs installation with GPU support in Windows 7

Hi, I've implemented the fix and I verified that it works on the command line; I've successfully complied the nvcc depend file. Nonetheless, CMake still fails on compiling in that stage. Here is the error message in Visual studio 2015 CMake Error at

Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

Since octane is not huge hydrocarbon, you could use LigParGen ( http://zarbi.chem.yale.edu/ligpargen/gmx_tutorial.html ) from Jorgensen's lab to generate an itp file for octane, which you could use as your guide to build an rtp. -Micholas === Micholas Dean Smith, PhD. MRSC

Re: [gmx-users] Error in NPT simulation

On 5/29/18 3:11 PM, Nagasree Garapati wrote: Dear all I am getting following error while running NPT simulation. I did energy minimization and NVT simulations, which ran successfully but when I proceed to NPT simulation, I am getting below error. Step 142, time 0.284 (ps) LINCS WARNING

Re: [gmx-users] topology

On 5/29/18 3:08 PM, mostafa paknia wrote: Hi I have two topology files already One of them is CNT's topology & otherone is a drug topology I want to make them just one How can i do that I already answered this a few days ago:

[gmx-users] Error in NPT simulation

Dear all I am getting following error while running NPT simulation. I did energy minimization and NVT simulations, which ran successfully but when I proceed to NPT simulation, I am getting below error. Step 142, time 0.284 (ps) LINCS WARNING relative constraint deviation after LINCS: rms

Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

On 5/29/18 3:08 PM, Atila Petrosian wrote: I know your mean. But there is not octane residue type in rtp file. Then you'll have to make one, using the existing molecules as a guide. The OPLS atom types for such a species should be straightforward to assign. -Justin --

[gmx-users] topology

Hi I have two topology files already One of them is CNT's topology & otherone is a drug topology I want to make them just one How can i do that -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

I know your mean. But there is not octane residue type in rtp file. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

On 5/29/18 2:50 PM, Atila Petrosian wrote: I did what was in README for octane molecule, but: Fatal error: Residue 'LIG' not found in residue topology database. Your input coordinates use a generic name (that most model-building programs use) that pdb2gmx doesn't recognize. Rename

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

I did what was in README for octane molecule, but: Fatal error: Residue 'LIG' not found in residue topology database. -- 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] md simulation of oil hydrocarbon / L-OPLS

On 5/29/18 2:43 PM, Atila Petrosian wrote: Dear Justin, I found L-OPLS in GitHub: https://github.com/wesbarnett/lopls Can I use it directly for hydrocarbon such as octane? I have no experience with those parameters. Test them and make sure they reproduce what's in the paper. -Justin

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

Dear Justin, I found L-OPLS in GitHub: https://github.com/wesbarnett/lopls Can I use it directly for hydrocarbon such as octane? -- 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] md simulation of oil hydrocarbon / L-OPLS

On 5/29/18 2:30 PM, Atila Petrosian wrote: Hi, I found a paper entitled " Optimization of the OPLS-AA Force Field for Long Hydrocarbons " (https://pubs.acs.org/doi/abs/10.1021/ct200908r). They obtained L-OPLS force field. Which version of gromacs has L-OPLS force field? None, you'll have

[gmx-users] md simulation of oil hydrocarbon / L-OPLS

Hi, I found a paper entitled " Optimization of the OPLS-AA Force Field for Long Hydrocarbons " (https://pubs.acs.org/doi/abs/10.1021/ct200908r). They obtained L-OPLS force field. Which version of gromacs has L-OPLS force field? -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Periodic Molecules

Thanks Justin. On Tue, May 29, 2018 at 11:09 AM, Justin Lemkul wrote: > > > On 5/29/18 12:04 PM, Lakshman Ji Verma wrote: > >> Thanks Justin. A follow up question for my better understanding. >> >> Does it mean that with “periodic-molecules” False, the periodic images >> won’t affect

Re: [gmx-users] Periodic Molecules

On 5/29/18 12:04 PM, Lakshman Ji Verma wrote: Thanks Justin. A follow up question for my better understanding. Does it mean that with “periodic-molecules” False, the periodic images won’t affect interactions in the actual simulation box, whereas they will affect if I keep “periodic-molecules”

Re: [gmx-users] Periodic Molecules

Thanks Justin. A follow up question for my better understanding. Does it mean that with “periodic-molecules” False, the periodic images won’t affect interactions in the actual simulation box, whereas they will affect if I keep “periodic-molecules” True? Thanks Lakshman On Tue, May 29, 2018 at

Re: [gmx-users] Periodic Molecules

On 5/29/18 11:50 AM, Lakshman Ji Verma wrote: What difference it will make I keep Periodic molecules option True or False? I read the manual but couldn’t understand more than keeping it False will be faster. The "periodic-molecules" option is for use with "infinite" systems like CNT,

[gmx-users] Periodic Molecules

What difference it will make I keep Periodic molecules option True or False? I read the manual but couldn’t understand more than keeping it False will be faster. Thanks! Lakshman -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Shifting in minimization

Hi, Sure, that's what trjconv -pbc and -ur are used for. There's no way to ask mdrun to automatically do the particular operation you want. Mark On Tue, May 29, 2018 at 3:21 PM Alex wrote: > Hi Mark, > Thanks. > The problem is that only the slab shifts and water molecules stay x-y > centrally

Re: [gmx-users] Shifting in minimization

Hi Mark, Thanks. The problem is that only the slab shifts and water molecules stay x-y centrally in the box. Similar to the picture in the link below: https://drive.google.com/open?id=1TwkgpesJPfFUiqxhl9rXBU33dwWn-tyD Regards, Alex On Fri, May 25, 2018 at 5:30 AM, Mark Abraham wrote: > Hi, > >

[gmx-users] Force Field Parameters

Hi, i am trying to parametrize a Metal-Organic-Framework for later gromacs simulations. Does anybody have experience in deriving parameters like force constants completely from theory? I know that there are techniques doing it with DFT-calculations but i would like to know other methods as

Re: [gmx-users] how to select backbone of martini protein cg

i have followed this tutorial http://cgmartini.nl/index.php/tutorials-general-introduction/proteins On 5/29/18, SHAHEE ISLAM wrote: > hi, > i want to calculate the contact between the backbone of protein(it is > a coarse grained protein using martini force field).how i will make > .ndx file to

[gmx-users] how to select backbone of martini protein cg

hi, i want to calculate the contact between the backbone of protein(it is a coarse grained protein using martini force field).how i will make .ndx file to calculate the contact. thanking you shahee islam university of calcutta -- Gromacs Users mailing list * Please search the archive at