[gmx-users] importance of nvlink in GPU nodes?

Dear users: does anybody know if the presence of either CPU-to-GPU or GPU-to-GPU nvlink affects the performance or efficiency of gromacs? Thank you, Chris. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

Re: [gmx-users] Replica Exchange for surface tension

On 3/28/17 2:59 PM, gozde ergin wrote: I use Charmm36 force field. Do you mean the force field parameter between cocobetaine and SDS? Because for pure surfactant I am able to estimate the correct surface tension. Which means force field parameter of SDS-water and cocobetaine-water is fine.

Re: [gmx-users] Replica Exchange for surface tension

I use Charmm36 force field. Do you mean the force field parameter between cocobetaine and SDS? Because for pure surfactant I am able to estimate the correct surface tension. Which means force field parameter of SDS-water and cocobetaine-water is fine. Sent from my iPhone > On 28 Mar 2017, at

Re: [gmx-users] MD for inorganic compound

Fixed charges may work as well, although some parameterization might be necessary. there are plenty of papers reporting such simulations, for instance: Langmuir, 2015, 31 (48), pp 13127–13137 *DOI: *10.1021/acs.langmuir.5b03167 On Tue, Mar 28, 2017 at 2:27 PM, Michael Brunsteiner

Re: [gmx-users] Help in a thermalization

It worked. Thanks Justin. 2017-03-27 18:23 GMT-03:00 Justin Lemkul : > > > On 3/27/17 5:17 PM, Graziele Bortolini wrote: > >> The error 3 was solved, but when I change to cutoff-scheme = group, I >> receive: >> >> "Fatal error: >> The largest charge group contains 66 atoms. The

[gmx-users] MD for inorganic compound

> Anjali Patel wrote:> What is the procedure of using gromacs specially for > inorganic compound??> I am beginner for gromacs simulation package, I used it > for organic > compounds. But unable to understand how to deal with inorganic compounds > and what about the force field and solvent we can

Re: [gmx-users] Replica Exchange for surface tension

On 3/28/17 12:43 PM, gozde ergin wrote: I have a mixed system of SDS and cocobetaine on water surface. I estimated the surface tension of SDS on water surface and cocabetaine on surface tension separately and correctly (comparing with experimental results). However I could not estimate the

Re: [gmx-users] About msd and lateral diffussion command

On 3/28/17 12:17 PM, Poncho Arvayo Zatarain wrote: Hello gromacs user: I want to obtain the msd and lateral diffussion for dppc/dppe membranes. I have this command: gmx msd -f file.tpr -s file.xtc -lateral z -rmcomm -beginfit 2 -endfit 13 -o msd.xvg <<< 2 3. Where 2 & 3 are dppc and

[gmx-users] Replica Exchange for surface tension

I have a mixed system of SDS and cocobetaine on water surface. I estimated the surface tension of SDS on water surface and cocabetaine on surface tension separately and correctly (comparing with experimental results). However I could not estimate the correct surface tension for SDS-cocobetaine

[gmx-users] About msd and lateral diffussion command

Hello gromacs user: I want to obtain the msd and lateral diffussion for dppc/dppe membranes. I have this command: gmx msd -f file.tpr -s file.xtc -lateral z -rmcomm -beginfit 2 -endfit 13 -o msd.xvg <<< 2 3. Where 2 & 3 are dppc and dppe. Wht do you think about my command? It´s ok or

Re: [gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?

- Message from Mark Abraham -     Date: Tue, 28 Mar 2017 12:04:42 +     From: Mark Abraham Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic SASA separately in latest

Re: [gmx-users] protein-ligand

Yeah. Thank you Mr.Justin On Tue, Mar 28, 2017 at 7:43 PM, Justin Lemkul wrote: > > > On 3/28/17 10:06 AM, RAHUL SURESH wrote: > >> But in case of charmm36ff, the script file will not generate .gro file for >> ligand I believe. In that case how will i generate gro file? >> >>

Re: [gmx-users] protein-ligand

On 3/28/17 10:06 AM, RAHUL SURESH wrote: But in case of charmm36ff, the script file will not generate .gro file for ligand I believe. In that case how will i generate gro file? I responded to your exact same question yesterday. Please read that. -Justin On Tue, Mar 28, 2017 at 5:28 PM,

Re: [gmx-users] protein-ligand

But in case of charmm36ff, the script file will not generate .gro file for ligand I believe. In that case how will i generate gro file? On Tue, Mar 28, 2017 at 5:28 PM, Justin Lemkul wrote: > > > On 3/27/17 11:49 PM, RAHUL SURESH wrote: > >> How will I add ligand .gro file in

Re: [gmx-users] Pull Code constant value

I suggest trial and error in quite short runs without wasting time on waiting for next day or so. Really large k can create segmentation faults or "cannonball into wall" like effects in MD movie. On Tuesday, March 28, 2017 2:43 PM, Souparno Adhikary wrote: Hi

Re: [gmx-users] Bond energy difference between CHARMM and GROMACS

Hi, Avoiding these kind of artefacts is exactly why the recommended procedure is to follow http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy Mark On Tue, Mar 28, 2017 at 2:02 PM Justin Lemkul wrote: > > > On 3/28/17 4:26 AM, Erik Marklund wrote: > > Dear Yvon,

Re: [gmx-users] Fwd: How to calculate Hydrophobic and Hydrophilic SASA separately in latest version of gromacs?

Hi, Did http://manual.gromacs.org/documentation/2016.3/user-guide/cmdline.html#g-sas help? Mark On Tue, Mar 28, 2017 at 7:31 AM wrote: > > > > -- Forwarded message -- > From: sp...@iacs.res.in > To: gmx-us...@gromacs.org > Cc: > Bcc: > Date: Fri, 24 Mar

Re: [gmx-users] dihedral restrains fail in free energy calculation

On 3/28/17 6:07 AM, Ahmet Yıldırım wrote: Dear users, I was trying to do the free energy calculation on GROMACS-2016.1 but I faced a problem. To apply intermolecular restraints I add the [ intermolecular_interactions ] part at the end of complex topology file. First I turn off intermolecular

Re: [gmx-users] MD for inorganic compound

On 3/28/17 5:00 AM, Anjali Patel wrote: What is the procedure of using gromacs specially for inorganic compound?? I am beginner for gromacs simulation package, I used it for organic compounds. But unable to understand how to deal with inorganic compounds and what about the force field and

Re: [gmx-users] topology

On 3/27/17 11:51 PM, RAHUL SURESH wrote: So it is mandatory to add *; Include ligand topology #include "drug.itp"* In top file.? You can't simulate a drug molecule without telling grompp what it's parameters are so that mdrun can simulate it. -Justin On Tue, 28 Mar 2017 at 2:08

Re: [gmx-users] protein-ligand

On 3/27/17 11:49 PM, RAHUL SURESH wrote: How will I add ligand .gro file in protein .gro file to make a complex .? With a text editor. Go through my tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html -Justin On Tue, 28 Mar 2017 at 2:12

Re: [gmx-users] Bond energy difference between CHARMM and GROMACS

On 3/28/17 4:26 AM, Erik Marklund wrote: Dear Yvon, Are you sure you ‘re not constraining, say, H-bonds in one and not the other? This is almost certainly the case. We've done extensive validation of CHARMM vs. GROMACS energies and the agreement is nearly perfect if calculated properly.

Re: [gmx-users] forcefield installation on GROMACS 5.1.4

On 3/28/17 3:12 AM, Simon Kit Sang Chu wrote: Dear Justin, Thank you very much. I followed the same spirit and add forcefield.doc. However, it did not work until changing all ffPACE_1.5.rtp .ddb .etc files into aminoacids.rpt .ddb . GROMACS seems to recognize only the name

Re: [gmx-users] Regarding Glycine structure

On 3/27/17 11:34 PM, Dilip H N wrote: Sorry it was a typing mistake..it is actually 1] To make indexes:- gmx make_ndx -f md.gro -o Hn-OW.ndx del 2 Removed group 2 'SOL' > del 1 Removed group 1 'Water' > del 0 Removed group 0 'System' a H1 H2 H3 OW Found xxx atoms with name H1 H2 H3 OW

[gmx-users] Pull Code constant value

Hi all, I am trying to pull a DNA molecule out of its binding pocket in a protein. I took Justin Lemkul's tutorial as the guiding script and started with k1 value of 1000. As it seemed, it needed more force to detach the molecule from its binding partner. Can you tell me how to estimate/calculate

[gmx-users] rotation while pulling

Hi All, {apologies if posted multiple times; seems like some trouble with my account} I want to pull linear molecule across the membrane in two ways allowing: - translation along Z and rotation around Z - translation along Z and rotation in all axes My current mdp-setting pulls molecular along

[gmx-users] dihedral restrains fail in free energy calculation

Dear users, I was trying to do the free energy calculation on GROMACS-2016.1 but I faced a problem. To apply intermolecular restraints I add the [ intermolecular_interactions ] part at the end of complex topology file. First I turn off intermolecular interactions and then turn them on one by one.

Re: [gmx-users] solvate with hexagonal box

Done! https://redmine.gromacs.org/issues/2148 On 28 Mar 2017, at 10:24, Erik Marklund > wrote: Hi Mark, Thanks. I will do so once my collaborators confirm that it’s ok that I upload the structure files. Kind regards, Erik

[gmx-users] performance issue with many short MD runs

Thanks Peter and Mark! I'll try running on single cores ... however, comparing the timings I believe the bottleneck might be the time spent in I/O(reading/writing to disk) and here running several jobs on a single node with multiple coresmight make things even worse. also funny: In the log

[gmx-users] MD for inorganic compound

What is the procedure of using gromacs specially for inorganic compound?? I am beginner for gromacs simulation package, I used it for organic compounds. But unable to understand how to deal with inorganic compounds and what about the force field and solvent we can use. With regards Anjali Patel

Re: [gmx-users] Align a vector with an axis of the box

Hi All and thank you Mark for your answer, I created a vector with make_ndx between 2 atoms but I can't find how to use this vector with the editconf command. The "rotate" option needs for a vector representing the rotation around axis Z ( 0 , 0 , 60) but the result seems not to be of this

Re: [gmx-users] Bond energy difference between CHARMM and GROMACS

Dear Yvon, Are you sure you ‘re not constraining, say, H-bonds in one and not the other? Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539

Re: [gmx-users] solvate with hexagonal box

Hi Mark, Thanks. I will do so once my collaborators confirm that it’s ok that I upload the structure files. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471

Re: [gmx-users] forcefield installation on GROMACS 5.1.4

Dear Justin, Thank you very much. I followed the same spirit and add forcefield.doc. However, it did not work until changing all ffPACE_1.5.rtp .ddb .etc files into aminoacids.rpt .ddb . GROMACS seems to recognize only the name "aminoacids". Also, don't forget to change the ffPACE1.5.itp

Re: [gmx-users] Bond energy difference between CHARMM and GROMACS

The correct value for kcal conversion is 4.184, however that does not explain the difference. Maybe you can try to take one exampel, e.g. the first one and test it bond by bond (by turning on one term at a time in the topology). I assume this is for 0 steps of MD or EM? Den 2017-03-28 kl.