Re: [gmx-users] Error: Atomtype CH2 not found

with atomname2type.n2t I should be able to post the sequence of events if you think it useful to others. Paul > On Dec 15, 2019, at 11:39 AM, Justin Lemkul wrote: > > > > On 12/14/19 1:14 PM, Paul Buscemi wrote: >> If the itp is correct then modify atomnames2types to

Re: [gmx-users] Young's modulus

Use surface tension in one direction. Measure increase in box size in that direction for YM. Restrain the bottom layer apply ST to top for SM PB > On Dec 15, 2019, at 3:25 AM, David van der Spoel wrote: > >> Den 2019-12-15 kl. 09:09, skrev Iman Katouzian: >> Good day, >> How can I calculate

Re: [gmx-users] Problem with GROMAC 2019.4

Great! What magic did you conjure up? PB > On Dec 13, 2019, at 12:56 PM, Avi Hundal wrote: > > Hi Paul, > > Yes sir, I am up and running. Thank you all! > > Regards, > > Avneel S. Hundal > > Email: havn...@gmail.com > > >> On Su

Re: [gmx-users] Error: Atomtype CH2 not found

If the itp is correct then modify atomnames2types to add the correct bonds and bond lengths PB > On Dec 13, 2019, at 7:52 PM, Justin Lemkul wrote: > > > >> On 12/13/19 2:18 AM, Muthusankar wrote: >> Dear Gromacs users, >> I am simulating a protein-ligand complex and performing the grompp

Re: [gmx-users] GPU performance, regarding

What does nvidia-smi tell you? PB > On Dec 12, 2019, at 7:30 AM, John Whittaker > wrote: > > Hi, > >> Hi Users. >> >> I am simulating a peptide of 40 residues with small molecules using oplsaa >> ff in Gromacs 2018.20 installed in CUDA environment.. The workstation has >> 16 Cores and 2

Re: [gmx-users] Regarding system shrunk

You did not mention the type of surface, but in real life an extruded polymer is under stress and you must restrain the ends. As in real life a heated uncrosslinked polymer will shrink. The system probably behaved appropriately PB > On Dec 9, 2019, at 11:31 AM, Mijiddorj B wrote: > > Dear

Re: [gmx-users] Problem with GROMAC 2019.4

> > Email: havn...@gmail.com > > >> On Sat, Dec 7, 2019 at 6:39 PM Paul Buscemi wrote: >> >> A shot in the dark. Cuda may not work with latest version of gcc. There is >> lit on this issue Try the repository version for cuda toolbox >> >> PB

Re: [gmx-users] Problem with GROMAC 2019.4

A shot in the dark. Cuda may not work with latest version of gcc. There is lit on this issue Try the repository version for cuda toolbox PB > On Dec 4, 2019, at 4:25 AM, Christian Blau wrote: > > HI Avneel, > > > In general, using the latest stable version is always the first thing to >

Re: [gmx-users] CA ions

Can you not use pdb2gmx with a pdb of Ca. Then create the itp from the new top. Add that as an include. Need to do the same with Cl for charge neutrality PB > On Dec 6, 2019, at 7:34 PM, Tasneem Kausar wrote: > > You are going to the right way. There are more options given in gmx genion. >

Re: [gmx-users] c2075 is not detected by gmx

take a look at https://docs.nvidia.com/cuda/cuda-memcheck/index.html <https://docs.nvidia.com/cuda/cuda-memcheck/index.html> make sure the GPU is functioning correctly with CUDA > On Nov 24, 2019, at 4:32 PM, paul buscemi wrote: > > Did you install the CUDA toolbox and dri

Re: [gmx-users] c2075 is not detected by gmx

Did you install the CUDA toolbox and drivers ? What is the output from "nvidia-smi" ? > On 24,Nov 2019, at 1:31 PM, Mahmood Naderan wrote: > > Hi > I have build 2018.3 in order to test that with c2075 GPU. > I used this command to build it > $ cmake .. -DGMX_GPU=on

Re: [gmx-users] How to build and simulate POPE/POPG bilayer with gromos54a7 force field

You might try the ATB website http://atb.uq.edu.au/molecule.py?molid=368385#panel-md you can create the lipid and submit your pdb ,but most likely it already exists in their data base. Use the modified Gromos54a7 ff and the pdb and itp provided by ATB.. Good luck ! Paul > On Nov 4,

Re: [gmx-users] simulating glass materials using GROMACS

Use this site for starters https://erastova.xyz/ it will move you toward your goal Paul > On Oct 12, 2019, at 2:03 PM, Alex Mathew wrote: > > Dear experts, > I would like to simulate NASICON type glass using GROMACS. The paper I > referred to here used LAMPP

Re: [gmx-users] Application of External Forces on Lipid Membrane

Would the application of surface tension work for you ? > On 6,Sep 2019, at 5:45 PM, Shivam Suthendran wrote: > > Hi there, > > I just completed the tutorial for KALP in DPPC membrane. I'm wondering > how I would go about the application forces on the lipid membrane. Any and > all input would

Re: [gmx-users] best performance on GPU

whoops ---not moo ( iphone took over ) but mpi…. > On Aug 2, 2019, at 5:09 PM, Paul Buscemi wrote: > > Why run moo on a single node ? > > PB > >> On Aug 1, 2019, at 5:53 PM, Mark Abraham wrote: >> >> Hi, >> >> We can't tell whether

Re: [gmx-users] simulation on 2 gpus

ommand you used or > telling how did you balance the work between cpu and gpu? > > What about pinning? Does anyone know how to deal with a cpu topology like > the one reported in my previous post and if it is relevant for performance? > Thanks > Stefano > > Il giorno sabato

Re: [gmx-users] simulation on 2 gpus

I run the same system and setup but no nvlink. Maestro runs both gpus at 100 percent. Gromacs typically 50 --60 percent can do 600ns/d on 2 atoms PB > On Jul 25, 2019, at 9:30 PM, Kevin Boyd wrote: > > Hi, > > I've done a lot of research/experimentation on this, so I can maybe get you >

Re: [gmx-users] best performance on GPU

Why run moo on a single node ? PB > On Aug 1, 2019, at 5:53 PM, Mark Abraham wrote: > > Hi, > > We can't tell whether or what the problem is without more information. > Please upload your .log file to a file sharing service and post a link. > > Mark > >> On Fri, 2 Aug 2019 at 01:05, Maryam

Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

Run with a maxwarn 1. If it runs then there is a deeper problem. If does not go it's probably a typo. Bet it's the latter PB > On Aug 1, 2019, at 2:52 PM, Justin Lemkul wrote: > > > >> On 8/1/19 3:50 PM, Mohammed I Sorour wrote: >> Dear Gromacs users, >> >> I'm running MD simulation on a

Re: [gmx-users] Self-interaction across periodic boundaries

Possibly turn pbc off and use nvt PB > On Jul 8, 2019, at 1:31 PM, Salman Zarrini wrote: > > Thanks Mark. > The problem is that I would like to keep the overall concentration > constant, so, using a larger box e.g. with 2 times larger lateral box > dimensions, > needs me to increase the

Re: [gmx-users] clustering of ions during NPT simulation

Are you sure you want 1m And not 0.1? PB > On Jun 27, 2019, at 2:44 PM, Netaly Khazanov wrote: > > Hi All, > I perform simulation of a transmembrane protein in a membrane in 1M > concentration of NaCl. > During the simulation, I noticed that ions began to cluster and they are > not evenly

Re: [gmx-users] appropriate force fielf

Do it the easy way. Find some literature that approximates your simulation and-after verifying their results with more lit- replicate their work PB > On Jun 25, 2019, at 9:38 AM, starlight wrote: > > Hi, I want to perform some simulations to study the interaction of 2 very > small peptides

[gmx-users] dragging gro files into VMD

Dear Users, this is a semi-gromacs question. I can use a command line “ vmd protein.gro” to open a gro file, but if I use linux’s “open with vmd “ the file will flash on ( within vmd ) then off and vmd closes. I can drag the files to Pymol with no problems. Has anyone run across this

Re: [gmx-users] Membrane protein simulation isotropic vs semiisotropic

The pressure on a (real-life) membrane is not isotropic, edges are under tension. so using the p-couple “surface-tension” - with water layers is appropriate. If you use p-couple = isotropic you should end up with a micelle because the hydrophobic effects are significant. p > On Jun 14,

Re: [gmx-users] Xeon W family vs scalable

Hi, Unless you are studying large systems ( 10e6 atoms ) do as Carsten suggests. Get a good Intel or AMD 8 core and the best GPU you can afford. Don’t worry too much about the speed of the CPU either. 3.2 Ghz is fine. p > On Jun 9, 2019, at 6:43 AM, Kutzner, Carsten wrote: > > Hi, > >

[gmx-users] proper use of restraints

Dear Users, I’ve modeled a simple polymer ( nylon ), 600 atoms aligned in the x direction . I create a restraint file for one molecule using the top file indices and fx,fy fz = 1 0 0 then place 10 to 100 copies in a box On equilibration, they exhibit the expected hydrogen bonding

Re: [gmx-users] Use of Restraint itps

in the mdp ? so if my restraint is MOL.posres.itp , I would state “define = DMOL.posres.itp “ ? Paul > On May 22, 2019, at 9:16 PM, Justin Lemkul wrote: > > On Wed, May 22, 2019 at 9:53 PM paul buscemi wrote: > >> Justin, >> >> Thank you very much for the resp

Re: [gmx-users] Use of Restraint itps

Justin, Thank you very much for the response. Obviously grompp will apply the restraint to the argument of -r molecule.gro and the restraint.itp location is in the top file #include statement. ( my (ITP directory ).but how does grompp make the association between the -r argument

Re: [gmx-users] number of coordinates in coordinate file does not match topology

Gromacs is telling you what to do.Make a new top file I do not think you can start a pdb from other than position 1 and the top must match exactly. it is probably more straightforward to delete the chain and save the pdb. Use pdb2gmx to recreate the top. good luck > On 16,May 2019, at

Re: [gmx-users] Energy from a subgroup of molecules

for further analysis Paul > On Apr 11, 2019, at 5:57 PM, Justin Lemkul wrote: > > > > On 4/11/19 5:39 PM, paul buscemi wrote: >> Thank you for the response, Mark. >> >> I do use the rerun tactic, and this is not too bad for a small number of >> molecule

Re: [gmx-users] Energy from a subgroup of molecules

Thank you for the response, Mark. I do use the rerun tactic, and this is not too bad for a small number of molecules but is there a way to include the index information within the mdrun (rerun ) … something like gmx mdrun -s adsorb.ener_gp.tpr -rerun adsorb,npt.trr - n use_only.ndx ?

Re: [gmx-users] PDB file that can be read in Gromacs

As Justin has pointed out , this process is well documented and UNL is not often found in molecules. No matter what - you will have to do some leg work. Because I run into this almost daily, this may at least get you started. First try using x2top with a selected force field. If your

Re: [gmx-users] info about gpus

There is significant information on the web regarding this subject, but in general speed scales nicely with the umber of cores. Massive memory is not required. > On 31,Jan 2019, at 11:14 AM, Stefano Guglielmo > wrote: > > Dear all, > I am tryin to set a new workstation and I would like to

Re: [gmx-users] Itp for a longer molecule out of a shorter one

the ATB just gives a > semi-empirical parameterized FF which basically is just a TOP file template > for large molecules. > Best regards, > Alex > >> >> Hope this helps >> >> Paul Buscemi, Ph.D. >> UMN BICB >> >> -Original Message- >

Re: [gmx-users] Itp for a longer molecule out of a shorter one

; > ff. >> > Indeed I got the gromos54a7 FF for the shorter molecule (< 50 atoms) from > ATB, however for larger system (> 50 atoms) the ATB just gives a > semi-empirical parameterized FF which basically is just a TOP file template > for large molecules. >

Re: [gmx-users] x2top finds 10+ bonds on atoms

Found the problem, In using the -ff select option, x2top was being directed to an incorrect gromos54a7 .ff directory - not the one in the local directory - with an incorrect n2t. x2top was apparently doing its best to make something. > On Feb 7, 2019, at 7:07 PM, paul buscemi wr

[gmx-users] x2top finds 10+ bonds on atoms

Dear gms users, I’ve been using x2top for some time with success.. I recently taken a polymer whose itp was created with x2top and using the same 55a7 ff and re-ran it as a demo-tutorial. In leaning how to use x2to and atomname2type I expected the error “ Cannot find forcefield for atom

Re: [gmx-users] info about gpus

I’ve run these conditions recently. The scale from as single 1080ti to 2080ti is proportional to the core number. the increase I’ve seen with 1080+1080 is 1.3-1.5 times as fast and perhaps 1.3 -1.6 times as fast depending on the model. In a million atom membrane model the two 1080ti’s ran at

Re: [gmx-users] Density of a droplet in spherical coordinate

You MIGHT be able to use the vmd plugin membplugin to measure the density https://sourceforge.net/p/membplugin/wiki/Home/ treating the sphere as a membrane or if you know the total density and the radius you should be able to construct an

Re: [gmx-users] different nvidia-smi/gmx GPU_IDs

Szilard, Is the environmental variable set at build ? thanks Paul > On Jan 18, 2019, at 12:36 PM, Szilárd Páll wrote: > > Hi, > > The CUDA runtime tries (and AFAIK has always tried) to be smart about > device order which is what GROMACS will see in its detection. The > nvidia-smi monitoring

Re: [gmx-users] gmx 2019 running problems

One other suggestion: from the PPA repository, install the Nvidia 410 driver. Your Cuda 9 install may work with the 410 driver but more likely you will need to reinstall. cuda If so, install the CUDA 10 toolkit, but DO NOT use the toolkit to install the driver when asked, it will

Re: [gmx-users] gmx 2019 running problems

Tamas I’ve the same build as you (almost… 2 gpus ) I found good results using one change : from -nt 16 to-ntomp 4 which should map the GPU’s and tasks in the same manner, but may be handled differently by mdrun. These two versions run with different efficiency on my rig. Paul >

Re: [gmx-users] Results of villin headpiece with AMD 8 core

that is not optimized.I’ll work with your files tomorrow and let you know how it turns out— thanks Have a a great weekendPaulOn Jan 12, 2019, at 3:11 PM, Wahab Mirco wrote:Hi Paul,thanks for your reply.On 11.01.2019 23:20, paul buscemi wrote:Getting the ion and SOL concentration correct in the top

Re: [gmx-users] Results of villin headpiece with AMD 8 core

distribution that is not optimized. I’ll work with your files tomorrow and let you know how it turns out— thanks Have a a great weekend Paul > On Jan 12, 2019, at 3:11 PM, Wahab Mirco > wrote: > > Hi Paul, > > thanks for your reply. > > On 11.01.2019 23:20, paul buscemi w

Re: [gmx-users] Results of villin headpiece with AMD 8 core

Dear M, Yup the timestep is enormous, but the Gromacs demo used 0.005 ns. At that point the 2700 and the Ti started flinging waters molecules off into the ozone. For the very short runs at 0.005 ~1400 ns/day was being hit. Usually the ts I use is 0.002 Getting the ion and SOL

Re: [gmx-users] AMD 32 core TR

idth to the RAM. But this is told to affect only > memory hungry applications. Thus at this moment I think that this does not > effect much gmx runs. I hope to try an RT 2990WX (amd 32core) in 1-2 months. > > On 2019. 01. 04. 4:18, paul buscemi wrote: >> Tamas, thanks for the respons

Re: [gmx-users] Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04; upgraded with GTX1080TI

> On Jan 8, 2019, at 6:29 PM, paul buscemi wrote: > > I just built from a similar situation but also went to Ubuntu Mint Tara 19 , > cuda runtime 10 ( used the Nvidia web site .run version not the deb - do not > install the driver from the toolkit -- add the 410 driv

Re: [gmx-users] Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04; upgraded with GTX1080TI

I just built from a similar situation but also went to Ubuntu Mint Tara 19 , cuda runtime 10 ( used the Nvidia web site .run version not the deb - do not install the driver from the toolkit ) added the 410 driver from the PPA and the system is quite happy. I believe I ran across some

Re: [gmx-users] gmx hbond

Use VMD/extensions/hydrogen bonds > On Jan 6, 2019, at 11:01 AM, rose rahmani wrote: > > hi, > > I want to know the number of hydrogen bonds of amino acid with water in > different distances above surface. for example in first 0.2nm, in second > 0.2 nm(0.2-0.4 nm) above surface. how can i do

Re: [gmx-users] AMD 32 core TR

Tamas, thanks for the response. In previous posts I mention using a single gtx 1080ti, sorry for not making it clear in the last post. On the 8 core AMD and an Intel 6 core I am running Cuda 10 with Gromacs 18.3 with no issues. I believe the larger factor in the slowness of the 32 core was

Re: [gmx-users] Surface Energy calculation of polymeric materials

Consider using a test probe. For instance, a micelle of DPPC, or POPC may spread differently onto the various surfaces. Then contact area or and interaction energy may supply the necessary information. You might get lucky with a contact angle. Paul busce...@umn.edu > On Dec 22, 2018, at

Re: [gmx-users] error on opening gmx_mpi

, Shi Li wrote: > >> >> >> -- >> >> Message: 3 >> Date: Tue, 18 Dec 2018 21:51:41 -0600 >> From: paul buscemi >> To: "gmx-us...@gromacs.org" >> Subject: Re: [gmx-users] error on opening gmx_m

Re: [gmx-users] Install Gromacs from Debian/Ubuntu repository vs build from source

In addition to Justin’s comments, the repository version is not adapted to GPU/CUDA use and as such is good for only very small systems and so loses one of the great advantages over other MD programs. I is not bad as an introduction to Gromacs so do not be afraid of installing, working with

Re: [gmx-users] error on opening gmx_mpi

Shi, Thanks fo the note Yes, somehow - there is a version of gromacs 5 that is being summoned. I’ve got clean up my act a bit. A suggestion was made to try to use the mpi version because of the CPU I am using. gmx v18.3 was installed , but I removed its build and built the 19.1 beta

Re: [gmx-users] error on opening gmx_mpi

Justin, thank you very much for the rapid response. I read that the same way, but I’m a bit confused. Is "mdrun_mpi version 5.1.2 in /usr/bin” a result of an install of v5 of gromacs ( have not used that version ) or a result of an install of a v5 of mpi ? i.e. not sure where that came

Re: [gmx-users] Area compressibility modulus GMX

John Ain’t nothin’ silly about analyzing membranes. It’s an artform . Have you taken a look at Membplugin https://sourceforge.net/p/membplugin/wiki/Home/ it provides trajectory values for among other things thickness and area/lipid.

Re: [gmx-users] using dual CPU's

Carsten,THanks for the response. my mistake - it was the GTX 980 from fig 3. … I was recalling from memory….. I assume that similar results would be achieved with the 1060’s No I did not reset , my results were a compilation of 4-5 runs each under slightly different conditions on two

Re: [gmx-users] using dual CPU's

pastebin.com, or termbin.com -- especially the latter is > very handy for those who don't want to leave the command line just to > upload a/several files for sharing (i.e. try "echo "foobar" | nc > termbin.com ) > > -- > Szilárd > On Tue, Dec 11, 20

Re: [gmx-users] using dual CPU's

> On Dec 10, 2018, at 7:33 PM, paul buscemi wrote: > > > Mark, attached are the tail ends of three log files for > the same system but run on an AMD 8 Core/16 Thread 2700x, 16G ram > In summary: > for ntpmi:ntomp of 1:16 , 2:8, and auto selection (4:4) are 12.0, 8.

Re: [gmx-users] using dual CPU's

o I need to get it right. > > I'll do as you suggest and report the results for both systems and I > > really appreciate the assist. > > Paul > > UMN, BICB > > > > On Dec 9 2018, at 4:32 pm, paul buscemi wrote: > > > > > > Dear Users, > > >

[gmx-users] using dual CPU's

Dear Users, I have good luck using a single GPU with the basic setup.. However in going from one gtx 1060 to a system with two - 50,000 atoms - the rate decrease from 10 ns/day to 5 or worse. The system models a ligand, solvent ( water ) and a lipid membrane the cpu is a 6 core intel i7 970(

Re: [gmx-users] Building Gromacs

This may be entirely misleading, but I have Gromacs 2018.3 loaded onto a SSD. This seems to be quite portable between machines I have access to ( during some builds ) ranging from an i5 4core, I7-8 core, i7-12 core and AMD 16 core 32 threads - all with expected scaling in speed and all cores

[gmx-users] And Ryzen 8 core/16 thread use

Dear Users, Does anyone have concerns/comments ( other than heat output of the processor ) in using the relatively new AMD Ryzen 7 2700 with Gromacs 18.3 or v19 and gromacs' ability to make use of the 16 threads along with a gtx1080ti ? thanks Paul -- Gromacs Users mailing list * Please

Re: [gmx-users] joining proteins at terminals

? I tried but the problem > persists. For my specific case I cannot add extra amino acids. I just have > to minimize the energy to pull them closer. > > Regards, > Simon Kit Sang Chu > Ph.D. student > Biophysics Graduate Group > University of California Davis > > > On W

Re: [gmx-users] joining proteins at terminals

Try giving residues in the macro-macro structure the same name … or possibly get rid of the 10A gap by using additional amino acids like gly-gly gly ? > On Oct 9, 2018, at 5:28 PM, Kit Sang Chu wrote: > > Hi everyone, > > I have a macromolecular structure which contains multiple copies of >

Re: [gmx-users] topology problem with x2top

> On Oct 4, 2018, at 8:30 AM, Paul Buscemi wrote: > > > > Maria > > Regarding PVDF ( in 54a7 ff) here is some information that may be useful: > === Input command to generate a 15 mer === > gb@RGB ~/Desktop/PVDF $ gmx x2top -f

Re: [gmx-users] topology problem with x2top

- It will be for 54a7 but maybe it will still provide some insight.. Not sure of how to approach the graphene, but I think Avogadro may have such a model. Unfortunately Avo does not provide top files. Paul Buscemi, Ph.D. Bioinformatics and Computational Chemistry University of Minnesota. > On 3,Oct 2018, a

[gmx-users] Polymer topology and MD Gromacs

ct: Re: [gmx-users] force field not found >> >> Yeah, if it is missing bonded parameters, you can always try to find >> something similar, at least with OPLS-AA -- don't really know about the >> other ff. >> >> Alex >> >> >> On 9/29/2018 8:58

Re: [gmx-users] force field not found

017. 121(16): p. 9022-9031. > > Alex > > On Thu, Sep 27, 2018 at 4:11 PM paul buscemi wrote: > >> Alex, >> >> There are so many important reactions / applications in which protein >> polymer interactions play a role that the ability to generate of >&

Re: [gmx-users] atom types not found

Alex, There are so many important reactions / applications in which protein polymer interactions play a role that the ability to generate of polymers should be part of gromacs repertoire. I’ll keep plugging away on this and report to the community if I can break the code - other than

Re: [gmx-users] atom types not found

CJ 0.142 CJ 0.142 > > and so on. A very useful utility for doing solid-state stuff with gmx. Hope > this helps. > > Alex > > > > The > > On Mon, Sep 24, 2018 at 7:48 PM Justin Lemkul wrote: > >> >> >> On 9/24/18 9:42 PM, paul busce

[gmx-users] atom types not found

given for PE some 9 years ago using a beginning, middle mers. But I need the rtp. Thanks for any responses Paul Buscemi, Ph.D. UMN -- 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] Center to center distance in cylindrical micelles

Shan, Load the .gro file into VMD , select the atoms/residues of interestsee: https://www.youtube.com/watch?v=QV0_CJHBF6U For a plot , You could try converting the trr file to text readable format with trjconv. From there select the atom numbers from each micelle that represent the

Re: [gmx-users] Using multiple GPU's

thing you've shown points to using both GPUs, but the relevant > output about the decision is not shown. > > Mark > > On Sat, Aug 11, 2018, 00:58 paul buscemi wrote: > >> Thanks Kevin. for the rapid response. >> >> I am using 2018. I’ll check the 2018 - ma

Re: [gmx-users] Using multiple GPU's

gromacs. If you are using v 5.1 (as the link suggests), strongly consider > upgrading to 2018. > > Kevin > > On Fri, Aug 10, 2018 at 12:57 PM, paul buscemi wrote: > >> >> Dear Uses, >> >> I’ve been following the examples on https://na01.safelink

[gmx-users] Using multiple GPU's

Dear Uses, I’ve been following the examples on http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html for setting up multiple GP’s but have not succeeded. Using a single GPU gmx runs well. Nvidia and gmx see the 2 PGUs. and I‘ve tried mdrun with variations of

Re: [gmx-users] Structure of polyvinyltoluene

Genevieve, Create a 3, 4 or 5 mer of the PVT and submit to ATB ( the wonderful topology makers ) to obtain the itp. ( 4A7 ff ) That wil give you the beginning middle and end mers for buiding a plymers as Justin has shown for PE. A second route is to build PVT under 500 atoms and submit

[gmx-users] topogen usage

Dear Users, Although topogen is a bit dated it seems to work well for ‘smaller’ polymers -500 atoms- and builds a single file itp. However in making a file for nylon 12 1000 atoms , a ‘central’ itp was create and separate files were made for section_dihedrals, section_bonds etc. Are these to

Re: [gmx-users] Slab gets bended in NVT

Alex, NPT appears to be doing exactly what it should esp if your slab is a membrane 1) are you using pcoupltype = surface tension with compressability = 4.5e-5 0 ?? 2) have your tried xy restraints on the ends of the slab Paul > On Jul 28, 2018, at 5:10 AM, Alex wrote: > > Dear

[gmx-users] Fwd: "Solved the issue on annealing - so to speak "

> > To work around the single point annealing I had to add three single groups. > Here I tried to use the first group as the ramp and the second two as constant > > > It turns out the number of groups the online definition gives and that mdp > wants is not the number of temperature groups

[gmx-users] possible bug in annealing

Dear Users, I’ve been trying to do a simple annealing with 1 group and two points. I receive the error below. Apparently gmx thinks there are three groups. If I comment out the annealing steps, the run proceeds normally . Total time of the run is 2 ns note: I’ve found the use of eg

[gmx-users] Compressing bundles of fibers into a surface

Dear gmx users I’m in the process of creating a PE polymer surface. pdb and itp files were obtained from ATB and were used to produce a (xyz) 142 x 6 x 60 A box ( starting size ) with 300 150 A long molecules. They were neatly aligned to start and - using pcoupletype = surface-tension

Re: [gmx-users] resize pre-equilibrated system

I believe this point is covered in either the Lysozyme or Kalp tutorials. However, You might try a smaller test system with any small protein like Kalp from the tutorials . Solvate it in a large( iso) box, minimize/equilibrate it, then resolvate that box in a smaller box. count the water

[gmx-users] use of surface tension

Dear users, I have set up a lipid membrane with its normal in the z direction. I would like to apply a surface tension only in the x ( or y) direction with the normal pressure at 1atm. that is - stretch the membrane in one direction I’ve modified npt mdp equilibrium file and have worked

Re: [gmx-users] Updated tutorials and new website

Justin, Thank you for all the hard work ! What can we do in return ??? Paul > On Jun 29, 2018, at 5:17 PM, Justin Lemkul wrote: > > > Hi All, > > I have updated all of my tutorials for use with GROMACS 2018. They are now > hosted on a new site: > > http://www.mdtutorials.com/gmx/ > >

Re: [gmx-users] GTX 960 vs Tesla K40

flops trumps clock speed….. > On Jun 13, 2018, at 3:45 PM, Alex wrote: > > Hi all, > > I have an old "prototyping" box with a 4-core Xeon and an old GTX 960. We > have a Tesla K40 laying around and there's only one PCIE slot available in > this machine. Would it make sense to swap the cards,

Re: [gmx-users] Gromacs 2018 and GPU

deas on how to access the > version of GROMACS that you want. Did you look there? > > Mark > > On Sun, May 6, 2018, 02:52 paul buscemi <pbusc...@q.com> wrote: > >> Mark, Justin >> >> I was able to access the GPU using simply : >> >&

Re: [gmx-users] Gromacs 2018 and GPU

rk). > > Mark > > On Sat, May 5, 2018, 00:55 Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 5/4/18 6:53 PM, paul buscemi wrote: >>> Justin, >>> >>> Here is the install script and a snippit from the log fi

Re: [gmx-users] Gromacs 2018 and GPU

gt; wrote: > > > > On 5/4/18 2:11 PM, paul buscemi wrote: >> Thank you Justin. >> >> Not at the linux system at the moment, but is there anything in particular I >> should look for in the log file ? > > Just look for "GPU" and you'll find it. >

Re: [gmx-users] Gromacs 2018 and GPU

Thank you Justin. Not at the linux system at the moment, but is there anything in particular I should look for in the log file ? Paul > On 4,May 2018, at 12:55 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 5/4/18 1:48 PM, paul buscemi wrote: >> thank you

Re: [gmx-users] Gromacs 2018 and GPU

format for a single GPU. thanks Paul > On 4,May 2018, at 11:57 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > > Hi, > > On Fri, May 4, 2018 at 6:43 PM paul buscemi <pbusc...@q.com > <mailto:pbusc...@q.com>> wrote: > >> >> >> I’ve b

[gmx-users] Gromacs 2018 and GPU

I’ve been struggling for a for several days to get Gromacs-2018 to use my GPU. I followed the INSTALL instructions ( several times ! ) that are provided in the 2018 tarball I know that the GPU ( GTX1080) is installed properly in that it works with Schrodinger and the Nvidia self tests.