Re: [gmx-users] Constraints applied for keeping rigid in ND

Hi Alex, Sorry for late reply. Because I could not find any reference of crystal CG mapping strategy, I parameterized my ND based on 4-1 mapping of the Martini CG model. Previously, I used default parameters and got an "oscillatory crystal" so I thought maybe I should try constraints. After talkin

[gmx-users] mail About LJ obtained by g_energy

Dear Justin  Thank you for your previous reply    When i run the g_energy tool to find out  LJ-SR nad Lj-SR between  CYCLIPEPTIDE1  anf CNT it shows the negative value  -311.9    and   -2.45122     wha is the meaning of  this Negative Value?If LJ-SR > LJ-LR then will

[gmx-users] Gas phase simulation

Dear Gromacs users, In order to estimate the free energy profile of water on organic coated-water system I am using Gromacs umbrella option. I put my water molecule far away from the bulk organic+water system and pulled this molecule through the bulk. When I checked the PMF profile I realized that

[gmx-users] ftp.gromacs.org not working now

I need this file: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gzthx -- 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)subscr

Re: [gmx-users] g_wham error in umbrella simulation

Hi, Justin Thanks a lot. Dos2unix works. There is even no blank space in every line. The problem is that I downloaded those .dat files from the internet, which were created in windows system. But I got another problem. Following your umbrella sampling tutorial, I got the PMF curve. The trend of

Re: [gmx-users] ftp.gromacs.org not working now

Try wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz Carsten > On 22 Apr 2015, at 13:30, Vytautas Rakeviius wrote: > > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lis

Re: [gmx-users] append does not work for me

On 4/21/15 10:41 AM, Michael Brunsteiner wrote: Hi, I just tried to continue a simulation, after having extended the total time using gmx convert-tpr -s original-xxx.tpr -o xxx.tpr -until 40 mdrun -nt 4 -deffnm xxx -cpi xxx.cpt xxx.cpt, xxx.log, and xxx.trr are present in the working d

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

On 4/21/15 6:54 AM, Christopher Neale wrote: Dear Mahender: It's a real pity that the pull_geometry = position has been removed. So now it's impossible to do umbrella sampling of a solute across a lipid bilayer properly? Anyway, I see a note about this removal here ( http://redmine.gromacs.

Re: [gmx-users] Extraction of the pdb data from the g_shame diagrams

On 4/21/15 1:24 PM, James Starlight wrote: and what the most trivial way to find correspondence of the line in the data file to what I actually see on the its graph (projection) ? Sorry I'm not an expert of xmgrace so it might seems for you trivial :) It's nothing to do with XmGrace. The g

Re: [gmx-users] mail About LJ obtained by g_energy

On 4/22/15 4:10 AM, vidhya sankar wrote: Dear Justin Thank you for your previous reply When i run the g_energy tool to find out LJ-SR nad Lj-SR between CYCLIPEPTIDE1 anf CNT it shows the negative value -311.9 and -2.45122 wha is the meaning of th

Re: [gmx-users] g_wham error in umbrella simulation

On 4/22/15 4:46 AM, Ming Tang wrote: Hi, Justin Thanks a lot. Dos2unix works. There is even no blank space in every line. The problem is that I downloaded those .dat files from the internet, which were created in windows system. But I got another problem. Following your umbrella sampling tutor

[gmx-users] Gromacs 5.0.4 Installation error

Hi all, While Trying to install GROMACS 5.0.4 with the following compiling arguments, during make i am getting the following error, I dont know how to solve it Please help me *# cmake .. -DGMX_THREAD_MPI=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.0.4-gpu -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=ON

[gmx-users] Fwd: Gas phase simulation

-- Forwarded message -- From: gozde ergin Date: Wed, Apr 22, 2015 at 12:21 PM Subject: Gas phase simulation To: gromacs.org_gmx-users@maillist.sys.kth.se Dear Gromacs users, In order to estimate the free energy profile of water on organic coated-water system I am using Gromacs u

[gmx-users] Variations of angles in a triclinic box

Dear Gromacs users, Recently I have used NPT ensemble with the following options in mdp file: Pcoupl = berendsen Pcoupltype = anisotropic tau-p= 1.0 1.0 1.0 0.0 0.0 0.0 compressibility = 1.0e-5 1.0e-5 1.0e-5 0.0 0.0 0.0 ref-p

Re: [gmx-users] Variations of angles in a triclinic box

Hi Antonio, You scale the axes separately. so you may stretch one component of a vector, and/or compress one, thus changing the angle. Cheers, Tsjerk On Wed, Apr 22, 2015 at 4:15 PM, Antonio Pizzirusso < antonio.pizziruss...@gmail.com> wrote: > Dear Gromacs users, > > Recently I have used NPT

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

Dear Justin: I think you are correct. It may not even really be that much of a hassle though one may need to be very careful in system setup for umbrellas near the center of the bilayer when using pull_start=yes rather than pull_coord1_init (i.e., one may need to make sure that the solute COM i

[gmx-users] lost information box after g_cluster

Dear Gromacs users, when I use g_cluster -f trajectory.xtc -s topology.tpr -g clusters.log -cl clusters.pdb -cutoff 0.05 (...) the obtained file clusters.pdb does not contain any information about the box. I have tried with .gro, and also with the option of g_cluster -pbc, but the dimensions of

Re: [gmx-users] calculating free energy

thanks for your anwers. On Tue, Apr 21, 2015 at 7:10 AM, lloyd riggs wrote: > > In general a realistic unfolded system would have to start at several > random points in state A, and allowing it to fold into state B. This > accounts for gaussian distributions of random states... > > these tend

[gmx-users] Order Parameters for alkyl chain

Dear gromacs users, I am new to gromacs and i am trying to determine the order parameter for my lipid alkyl chain carbon atoms. I had a pdb file containing co-ordinates for a number of individual lipid monomers that i performed the g_order command on to obtain a .ndx file. At this point i

Re: [gmx-users] Order Parameters for alkyl chain

dear sly, You can do that folow the tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/09_analysis.html Xuechuan At 2015-04-22 23:51:16, "Sylvester Tumusiime" wrote: Dear gromacs users, I am new to gromacs and i am trying

[gmx-users] help on Graphene Nano Sheets

Hi, i am trying to model a Graphene nano sheet GNS on Gromacs- I follow the advices about the nanotubes presented in the help site. _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_ I run this command to greate the topology: _g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_ I go

Re: [gmx-users] help on Graphene Nano Sheets

Hello, The forcefields for CNT and graphene are identical (for the purpose of this discussion). Two questions: 1. Where did you get the initial graphene structure? 2. Are there any CONECT statements in it? I assume you used Andrea Minoia's guide and the contents of your cnt2_oplsaa.ff directory

[gmx-users] Umbrella Sampling Error in Gromacs 5.0

Dear Users, I am trying to do a umbrella pulling of one lipid out of a bilayer using umbrella sampling code. In Gromacs 5.0, there is a big change in umbrella sampling implementation. I set my pull parameters like this: pull = umbrella pull_geometry = cylinder ; Pull in the directi

[gmx-users] using_gromacs_with_openmpi

Dear GROMACS users and developers I've compiled GROMACS 4.5.5 with gcc and *enable-mpi* option for a small cluster e.g 4 nodes on 1GbE network The code was compiled without problem and i can use it in sequential and parallel mode (using mpirun command), but the performance over the network is very

Re: [gmx-users] lost information box after g_cluster

On 4/22/15 11:18 AM, Rebeca García Fandiño wrote: Dear Gromacs users, when I use g_cluster -f trajectory.xtc -s topology.tpr -g clusters.log -cl clusters.pdb -cutoff 0.05 (...) the obtained file clusters.pdb does not contain any information about the box. I have tried with .gro, and also with

Re: [gmx-users] Order Parameters for alkyl chain

On 4/22/15 11:51 AM, Sylvester Tumusiime wrote: Dear gromacs users, I am new to gromacs and i am trying to determine the order parameter for my lipid alkyl chain carbon atoms. I had a pdb file containing co-ordinates for a number of individual lipid monomers that i performed the g_order comma

Re: [gmx-users] Umbrella Sampling Error in Gromacs 5.0

On 4/22/15 3:54 PM, Jianhui Tian wrote: Dear Users, I am trying to do a umbrella pulling of one lipid out of a bilayer using umbrella sampling code. In Gromacs 5.0, there is a big change in umbrella sampling implementation. I set my pull parameters like this: pull = umbrella pull_

Re: [gmx-users] using_gromacs_with_openmpi

On 4/22/15 3:59 PM, Hossein H wrote: Dear GROMACS users and developers I've compiled GROMACS 4.5.5 with gcc and *enable-mpi* option for a small cluster e.g 4 nodes on 1GbE network The code was compiled without problem and i can use it in sequential and parallel mode (using mpirun command), but

[gmx-users] membrane protein simulation

Dear Justin I am going to simulate a homo trimer trans-membrane protein; Base on the crystallographic structures there is 7 phosphatidyl glycerol phosphate (PGP) per each monomer and also 3 glycolipid molecules (S-TGA-1, or 3-HSO 3 -Galpβ1-6ManpR1-2GlcpR-1-archeol) located inside the trimer on the

Re: [gmx-users] using_gromacs_with_openmpi

isn't gigabyte Ethernet adequate even for 2 nodes? On Thu, Apr 23, 2015 at 12:36 AM, Justin Lemkul wrote: > > > On 4/22/15 3:59 PM, Hossein H wrote: > >> Dear GROMACS users and developers >> >> I've compiled GROMACS 4.5.5 with gcc and *enable-mpi* option for a small >> cluster e.g 4 nodes on 1Gb

Re: [gmx-users] membrane protein simulation

On 4/22/15 4:07 PM, Mostafa Javaheri wrote: Dear Justin I am going to simulate a homo trimer trans-membrane protein; Base on the crystallographic structures there is 7 phosphatidyl glycerol phosphate (PGP) per each monomer and also 3 glycolipid molecules (S-TGA-1, or 3-HSO 3 -Galpβ1-6ManpR1-2Gl

Re: [gmx-users] using_gromacs_with_openmpi

On 4/22/15 4:14 PM, Hossein H wrote: isn't gigabyte Ethernet adequate even for 2 nodes? Well, what does your benchmarking show you? Likely the performance degrades because the interconnect is simply too slow to benefit from additional CPU horsepower. -Justin On Thu, Apr 23, 2015 at 12

Re: [gmx-users] using_gromacs_with_openmpi

the performance degrades even when I only use two nodes!!! and the mdrun process uses almost 100% of CPU on each node On Thu, Apr 23, 2015 at 12:47 AM, Justin Lemkul wrote: > > > On 4/22/15 4:14 PM, Hossein H wrote: > >> isn't gigabyte Ethernet adequate even for 2 nodes? >> >> > Well, what does

Re: [gmx-users] append does not work for me

On 4/21/15 10:41 AM, Michael Brunsteiner wrote: >> >> Hi, >> I just tried to continue a simulation, after having extended the total time >> using >> >> gmx convert-tpr -s original-xxx.tpr -o xxx.tpr -until 40 >> mdrun -nt 4 -deffnm xxx -cpi xxx.cpt >> >> xxx.cpt, xxx.log, and xxx.trr are pres

Re: [gmx-users] append does not work for me

On 4/22/15 4:23 PM, Michael Brunsteiner wrote: On 4/21/15 10:41 AM, Michael Brunsteiner wrote: >> >> Hi, >> I just tried to continue a simulation, after having extended the total time using >> >> gmx convert-tpr -s original-xxx.tpr -o xxx.tpr -until 40 >> mdrun -nt 4 -deffnm xxx -cpi

Re: [gmx-users] using_gromacs_with_openmpi

On 4/22/15 4:24 PM, Hossein H wrote: the performance degrades even when I only use two nodes!!! and the mdrun process uses almost 100% of CPU on each node Like I said, any benefit you might theoretically get from multiple CPU is being undermined by latency in the gigabit ethernet connection

Re: [gmx-users] Umbrella Sampling Error in Gromacs 5.0

> > Date: Wed, 22 Apr 2015 16:05:18 -0400 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Umbrella Sampling Error in Gromacs 5.0 > Message-ID: <5537fefe.6020...@vt.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 4/22/15 3:54 PM, Jianhui

Re: [gmx-users] using_gromacs_with_openmpi

But I wonder if the the performance degrade due to network latency why mdrun process uses 100% CPU on each node!!! On Thu, Apr 23, 2015 at 1:05 AM, Justin Lemkul wrote: > > > On 4/22/15 4:24 PM, Hossein H wrote: > >> the performance degrades even when I only use two nodes!!! and the mdrun >> pro

[gmx-users] Pull code

Hi all, I have a group (DNA) I'd like to translate relative to the other group (CNT) along the Z-direction so that DNA is the only group that's actually moving. The code I had prior to what I have now worked under GMX 4.5.something. Since the syntax has changed in 5.0.x, I found Justin's old sugg

Re: [gmx-users] Pull code

Hi，Alex You can try constraint. In umbrella， both 2 groups move. Sent from my Huawei Mobile Alex wrote: Hi all, I have a group (DNA) I'd like to translate relative to the other group (CNT) along the Z-direction so that DNA is the only group that's actually moving. The code I had prior to wha

Re: [gmx-users] Pull code

Well, no, i don't want two. I want one! :) On Wed, Apr 22, 2015 at 5:17 PM, Ming Tang wrote: > Hi，Alex > > You can try constraint. In umbrella， both 2 groups move. > > Sent from my Huawei Mobile > > Alex wrote: > > Hi all, > > I have a group (DNA) I'd like to translate relative to the other gro

Re: [gmx-users] Pull code

On 4/22/15 7:17 PM, Ming Tang wrote: Hi，Alex You can try constraint. In umbrella， both 2 groups move. Not really. The constraint option keeps a rigid constraint between the two groups. The "umbrella" keyword specifies a harmonic potential, whose strength is tunable. Otherwise, the two

Re: [gmx-users] help on Graphene Nano Sheets

yes, i used the Minoia tutorial, i use a cnt_oplsaa at the first attempt, and forward i copied and modify the standard oplsaa folder. with both of them i have the same trouble. The inizial graphene layer was created using*VMD modelling toolbox*, that was a .pdb file, i convert it in .gro file

Re: [gmx-users] Umbrella Sampling Error in Gromacs 5.0

On 4/22/15 4:59 PM, Jianhui Tian wrote: Date: Wed, 22 Apr 2015 16:05:18 -0400 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella Sampling Error in Gromacs 5.0 Message-ID: <5537fefe.6020...@vt.edu> Content-Type: text/plain; charset=windows-1252; format=flowed On

Re: [gmx-users] help on Graphene Nano Sheets

You don't need to run x2top on the GRO file, you can apply it directly to the PDB. It seems like the PDB to GRO conversion destroyed the coordinates due to poor formatting of the initial coordinates. This has nothing to do with the forcefields or graphene, you may just have a crappy PDB. Alex On

Re: [gmx-users] help on Graphene Nano Sheets

On 4/22/15 7:22 PM, marcello cammarata wrote: yes, i used the Minoia tutorial, i use a cnt_oplsaa at the first attempt, and forward i copied and modify the standard oplsaa folder. with both of them i have the same trouble. The seg fault will always occur with version 5.0.4; there is a bug we

Re: [gmx-users] help on Graphene Nano Sheets

Justin, everything works for me with graphene/x2top under the latest version. Am I doing something wrong? :) On Wed, Apr 22, 2015 at 5:26 PM, Justin Lemkul wrote: > > > On 4/22/15 7:22 PM, marcello cammarata wrote: > >> yes, i used the Minoia tutorial, >> i use a cnt_oplsaa at the first attempt,

Re: [gmx-users] Pull code

Hi， Justin I will try whether i can set reference group using umbrella later. Sent from my Huawei Mobile Justin Lemkul wrote: On 4/22/15 7:17 PM, Ming Tang wrote: > Hi，Alex > > You can try constraint. In umbrella， both 2 groups move. > Not really. The constraint option keeps a rigid constra

Re: [gmx-users] Pull code

The CNT group is actually very strongly restrained, not the entire atomic population, but the edges. So, from inspecting my code, everything looks right? Thanks, Alex > >Not really. The constraint option keeps a rigid constraint between the > two groups. The "umbrella" keyword specifies a >h

Re: [gmx-users] Pull code

On 4/22/15 7:47 PM, Alex wrote: The CNT group is actually very strongly restrained, not the entire atomic population, but the edges. So, from inspecting my code, everything looks right? Yep. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirs

Re: [gmx-users] Pull code

Hi, Justin I am confusing about what is the difference between the rigid constraint in constraint pull method and the harmonic potential using umbrella. The force acts directly on the centre of mass of the group in constraint, and the force acts on the center of mass of the group through a sprin

Re: [gmx-users] Pull code

Hi, Alex I tried this code plus freeze all of the atoms in the group needed to stay in place, and it worked well. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Alex Sent: Thursday, 23 Apr

Re: [gmx-users] Pull code

On 4/22/15 8:03 PM, Ming Tang wrote: Hi, Justin I am confusing about what is the difference between the rigid constraint in constraint pull method and the harmonic potential using umbrella. The force acts directly on the centre of mass of the group in constraint, and the force acts on the ce

Re: [gmx-users] Pull code

That is not an option for me, all groups must exhibit full dynamics, so partial restraint seems like a decent option. It is my understanding that explicitly moving only one group is impossible in the new version. Is that the case? Thanks, Alex On Wed, Apr 22, 2015 at 5:58 PM, Ming Tang wrote:

Re: [gmx-users] Pull code

On 4/22/15 8:37 PM, Alex wrote: That is not an option for me, all groups must exhibit full dynamics, so partial restraint seems like a decent option. It is my understanding that explicitly moving only one group is impossible in the new version. Is that the case? No, you can (and have always

Re: [gmx-users] Pull code

Okay, that clarifies it. I wasn't sure, because of your earlier comment, despite the fact that I was using referenced pull. Indeed, in my case, part of the system is essentially solid-state, its COM fixed in space, while other stuff is being moved relative to it. I was also curious how (in more de

[gmx-users] gromacs installation fatal errors

Dear All, I just tried to install gromacs-5.0.4, and I got 2 fatal errors: 1. /gromacs-5.0.4/build/CMakeFiles/CmakeTmp/CheckIncludeFiles:c:16 fata error:io.h: No such file or directory 2. . /gromacs-5.0.4/Src/gromacs/legacyheader No such file or directory. I am looking forward to getting

[gmx-users] on the regression tests

Dear All, When I install gromacs-5.0.3, after the "make check" step, it indicates "Regression tests have not been run. If you want to run them from the build systems,get the correct version of the regression tests ackage and set REGRESSION_PATH in CMake to point to it, or set REGRESSIONTEST_DO

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

Thank you dear Justin and Christopher Neale for your help. Solute is at -z relative to the bilayer and wants to pull toward +z from the bulk water on the -Z to the +z bulk water through the membrane. I observed that the + and the - sign in the pull_coord1_rate is associated with increase or dec

Re: [gmx-users] membrane protein simulation

Hi Mostafa, We have a complete simulation system of bacteriorhodopsin in the purple membrane, which you can use as basis for your simulations if you want. Best, Tsjerk On Apr 22, 2015 10:08 PM, "Mostafa Javaheri" wrote: > Dear Justin > I am going to simulate a homo trimer trans-membrane protei

[gmx-users] Optimal GPU setup for workstation with Gromacs 5

Dear all, My workstation specs are 2 x Intel Xeon E5-2695v2 2.40 GHz, 12 Cores. I would like to combine this with an optimal GPU setup for Gromacs 5 running simulations with millions of atoms. May I know what are the recommended setups? My vendor proposed doing a dual K40 Tesla GPU setup, would

[gmx-users] Optimal GPU setup for workstation with Gromacs 5

Dear all, My workstation specs are 2 x Intel Xeon E5-2695v2 2.40 GHz, 12 Cores. I would like to combine this with an optimal GPU setup for Gromacs 5 running simulations with millions of atoms. May I know what are the recommended setups? My vendor proposed doing a dual K40 Tesla GPU setup, would

Re: [gmx-users] Variations of angles in a triclinic box

Dear Tsjerk, Thank you very much for your reply and valuable suggestions, Is possible to simulate using appropriate values in pressure parameters a triclinic box without varying the angles? 2015-04-22 16:19 GMT+02:00 Tsjerk Wassenaar : > Hi Antonio, > > You scale the axes separately. so you

[gmx-users] Problems in the modelling of interaction between peptide and copper

Dear all, I got a problem when modelling the interaction of a peptide and copper. I am using the force field of opls-aa. The charge of copper atoms are defined as zero and the non-bonded parameters are obtained from the CU ions, which can be found in opls-aa. I applied smd and found that the p

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

Hi Christopher Neale and Justin I used now following pull code (what i understood from the previous emails) to pull the drug across the membrane ; Pull code pull= umbrella pull_geometry= direction pull_dim= N N Y pull_coord1_vec=0 0 -1 pull_start= yes pull_ngroups=2 p