[gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.

Dear all, I used Gromacs 5.0.5 to generate a trajectory of polarizable water system with SWM4-NDP model, and then tried to use a custom version Gromacs 4.5.5 to calculate local pressure of the system. When I generate the .tpr file with Gromacs 4.5.5, an error coccurs: Fatal error: Incorrect

Re: [gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.

On 8/20/15 1:03 PM, 折晓会 wrote: Dear all, I used Gromacs 5.0.5 to generate a trajectory of polarizable water system with SWM4-NDP model, and then tried to use a custom version Gromacs 4.5.5 to calculate local pressure of the system. When I generate the .tpr file with Gromacs 4.5.5, an error

Re: [gmx-users] High load imbalance: 31.8%

Hi Anthony, Good choice, your admins should be able to help. Do emphasize when talking to them that you need your job to be placed as compact as possible, on the closest possible set of cores with the tightest possible affinity settings. Cheers, -- Szilárd On Thu, Aug 20, 2015 at 6:12 PM,

[gmx-users] High load imbalance: 31.8%

Hi all, I appear to have a very high load imbalance on some of my runs. Values starting from approx. 7% up to 31.8% with reported vol min/aver of around 0.6 (I haven¹t found one under half yet). When I look through the .log file at the start of the run I see: Initializing Domain Decomposition

[gmx-users] atom types IP and IM

Hi; I've used ff14sbamber force field to generate my system. As this force field doesn'texist in gromacs, I generated the first structure of my system withamber tools then I converted the topology and coordinate files intogromacs format by using acpype. (In the amber tools I've added NaClto my

Re: [gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.

On 8/20/15 6:05 PM, 折晓会 wrote: Thank you professor Justin! I solved this error which comes from the decimals of the box dimensions. Initially, my box dimensions are 4.5*4.5*16 nm3 and the local pressure calculation does not work, but after I change them to be integers 4*4*16 nm3 in the gro

Re: [gmx-users] AIX XLC Gromacs-5.1-rc1. Undefined reference. Underscore issue.

Hi, GROMACS 5.1 is out, please don't install 5.1-rc1 any more. There's a little bit of advice about using custom linear algebra libraries at http://manual.gromacs.org/documentation/5.1/install-guide/index.html#linear-algebra-libraries but you don't need to bother with such libraries unless you

Re: [gmx-users] Adding HSD residue to AMBER ff99SB-ILDN

On 8/20/15 3:17 AM, Simone Bolognini wrote: Hi everyone, I have a .pdb file of the WW domain of human FIP35 protein extracted from an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3. Now I need to obtain the topology out of it, but the .pdb contains a residue, namely HSD,

Re: [gmx-users] CHARMM forcefield parameters for carbon naotubes

On 8/20/15 7:53 AM, Sanchaita Rajkhowa wrote: Dear all, I am trying to simulate a carbon nano-tube using CHARMM27 forcefield but I can't get it right. I have been following the modeling carbon nano-tubes with gromacs (http://chembytes.wikidot.com/grocnt) but it is done using opls-aa

Re: [gmx-users] Adding HSD residue to AMBER ff99SB-ILDN

Thank you for your answer! I did it and now gromacs throws me the following error: Atom HG1 in residue SER 2 was not found in rtp entry SER with 11 atoms while sorting atoms.. Any clue? Thank you very much. Il giorno gio 20 ago 2015 alle ore 13:18 Justin Lemkul jalem...@vt.edu ha scritto: On

Re: [gmx-users] High load imbalance: 31.8%

Hi, In cases like this, it's good to describe what's in your simulation, and share the full .log file on a file-sharing service, so we can see both the things mdrun reports early and late. Mark On Thu, Aug 20, 2015 at 8:22 AM Nash, Anthony a.n...@ucl.ac.uk wrote: Hi all, I appear to have a

Re: [gmx-users] trjconv -dt issue

Hi, This is indeed problematic. The .edr format (and its tools) are designed with limitations that were not really a problem 10 years ago. One of the limitations is that the time itself is stored in the same precision as the simulation data, and this starts to lose precision as the simulation

[gmx-users] CHARMM forcefield parameters for carbon naotubes

Dear all, I am trying to simulate a carbon nano-tube using CHARMM27 forcefield but I can't get it right. I have been following the modeling carbon nano-tubes with gromacs (http://chembytes.wikidot.com/grocnt) but it is done using opls-aa forcefield. I have tried in a similar way and I keep

Re: [gmx-users] Adding HSD residue to AMBER ff99SB-ILDN

Well... that was a rookie mistake. Sorry about that. Thank you! Il giorno gio 20 ago 2015 alle ore 14:18 Justin Lemkul jalem...@vt.edu ha scritto: On 8/20/15 8:16 AM, Simone Bolognini wrote: Thank you for your answer! I did it and now gromacs throws me the following error: Atom HG1 in

Re: [gmx-users] Error while configuring gmx-3.3.1

Hi, Apparently the 3.3.1 install isn't working well for you. You can use cp -R gromacs-3.3.1/share/top/* /usr/local/gromacs/share/top/ which is a standard unix command. Mark On Thu, Aug 20, 2015 at 5:52 AM Padmani Sandhu padmanisandh...@gmail.com wrote: Hello Justin, I have copied both the

[gmx-users] A query about nsteps

Dear gromcas users, I carried out a continuation of previous md run for nsteps of 500 and dt of 0.002 using the following commands, gmx grompp -f md.mdp -o md2.tpr -c md1.gro -t md1.cpt -r ref.pdb -n index.ndx -p topol.top gmx_mpi mdrun -cpi md1.cpt -deffnm md2 The mdp file following run

Re: [gmx-users] A query about nsteps

On 8/20/15 7:49 AM, anu chandra wrote: Dear gromcas users, I carried out a continuation of previous md run for nsteps of 500 and dt of 0.002 using the following commands, gmx grompp -f md.mdp -o md2.tpr -c md1.gro -t md1.cpt -r ref.pdb -n index.ndx -p topol.top gmx_mpi mdrun -cpi

Re: [gmx-users] Adding HSD residue to AMBER ff99SB-ILDN

On 8/20/15 8:16 AM, Simone Bolognini wrote: Thank you for your answer! I did it and now gromacs throws me the following error: Atom HG1 in residue SER 2 was not found in rtp entry SER with 11 atoms while sorting atoms.. Any clue? Thank you very much. pdb2gmx -ignh -Justin Il giorno gio

[gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...

Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm.

Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...

Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues.

Re: [gmx-users] Problem compiling Gromacs 5.1

Thanks, Peter. But , I mean I don’t know what line I should change to from line 52 of cmake/FindPhinx.cmake to solve this error. Leucer 2015/08/20 16:02、Kroon, P.C. p.c.kr...@rug.nl のメール： Just use your favourite text editor. Peter On Thu, Aug 20, 2015 at 3:10 AM,

Re: [gmx-users] Problem compiling Gromacs 5.1

Hi, You should change line 52 from what it is, to what I suggested - which inserts quotation marks around one of the variable interpolations. Mark On Thu, Aug 20, 2015 at 2:43 PM 岡部篤俊 atsutoshi0...@gmail.com wrote: Thanks, Peter. But , I mean I don’t know what line I should change to from

Re: [gmx-users] Problem compiling Gromacs 5.1

On 8/20/15 8:42 AM, 岡部篤俊 wrote: Thanks, Peter. But , I mean I don’t know what line I should change to from line 52 of cmake/FindPhinx.cmake to solve this error. Mark's message provided the corrected line. Just replace whatever is on line 52 with that. -Justin Leucer 2015/08/20

Re: [gmx-users] Respect waters in crystallographic pdb file?

And what about genion? Suppose I have to add some ions to the system to neutralize, so I use the following command: genion -s S_ion.tpr -o S_sol.gro -p S_sol.top -nn 1 -nname CL SOL Is there a chance that this replaces one of the original crytallographic waters with the CL? Thanks. Best,

Re: [gmx-users] Respect waters in crystallographic pdb file?

On 8/20/15 10:06 AM, Jorge Fernandez de Cossio Diaz wrote: And what about genion? Suppose I have to add some ions to the system to neutralize, so I use the following command: genion -s S_ion.tpr -o S_sol.gro -p S_sol.top -nn 1 -nname CL SOL Is there a chance that this replaces one of the

[gmx-users] inversion potential

Hi, Dear gromacs usersI want to define some bond parameters within opls-aa force field, which are taken from a paper. I know how to define nonbonded parameters as well as bonds and angles and dihedrals. But I don't know how to define a so-called inversion potential and the paper is vague on

Re: [gmx-users] trjconv -dt issue

Thanks for your explanation, Mark. Concerning energy files and eneconv: - I will try double-precision eneconv, as I don't mind larger files. - In reply to the advice to reset the time of the energy files: how to do it? eneconv has no option for this, although the help states: With one file

Re: [gmx-users] trjconv -dt issue

Hi, On Thu, Aug 20, 2015 at 4:00 PM Matthias Ernst matthias.er...@physik.uni-freiburg.de wrote: Thanks for your explanation, Mark. Concerning energy files and eneconv: - I will try double-precision eneconv, as I don't mind larger files. - In reply to the advice to reset the time of the

Re: [gmx-users] Error while configuring gmx-3.3.1

Thanks Mark, It worked. grompp working fine now. regards, Padmani On Thu, Aug 20, 2015 at 4:14 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Apparently the 3.3.1 install isn't working well for you. You can use cp -R gromacs-3.3.1/share/top/* /usr/local/gromacs/share/top/

[gmx-users] No Checkpoint File generated

Dear All, I am doing a md simulation for a system consisting of protein with 1.5ns thick water shell. The whole system is simulated in vacuum. I turn of PBC and cutoffs for nonbond interactions. Now, the simulation runs well, but no checkpoint file is output. Does anyone know the issue? The

Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded

Note that I am adding position restrains to fix all the termini of the incomplete fragments. Shouldn't that take care of the missing residues? -- Message: 5 Date: Thu, 20 Aug 2015 20:29:42 + From: Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu To:

Re: [gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.

On 8/20/15 4:01 PM, 折晓会 wrote: Thank you professor Justin! I solved this error with your suggestion. When I use mdrun -rerun to calculate the local pressure, another error occurs: Fatal error: Rerun trajectory frame step 60 time 600.00 has too small box dimensions What does this

Re: [gmx-users] What's the point of adding ions to neutralize the system?

On 8/20/15 4:15 PM, Victor Rosas Garcia wrote: You said it yourself: to neutralize the net charge of the system. Great answer: you neutralize the system in order to neutralize the system :) Since the ion added is usually very far away from the protein (or molecule of interest), I don't

Re: [gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.

Thank you professor Justin! I solved this error with your suggestion. When I use mdrun -rerun to calculate the local pressure, another error occurs: Fatal error: Rerun trajectory frame step 60 time 600.00 has too small box dimensions What does this mean? Best wishes, Xiaohui Date:

Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...

Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when

Re: [gmx-users] High load imbalance: 31.8%

Hi Mark, Many thanks for looking into this. One of the log files (the job hasn’t finished running) is here: https://www.dropbox.com/s/zwrro54yni2uxtn/umb_3_umb.log?dl=0 The system is a soluble collagenase in water with a collagen substrate and two zinc co-factors. There are 287562 atoms in the

Re: [gmx-users] High load imbalance: 31.8%

Hi, You're not pinning threads and it seems that you're running on a large SMP machine! Assuming that the 512 threads reported (line 91) is correct that's a 32 socket SMP machine, perhaps an SGI UV? In any case Xeon E5-4xxx is typically deployed in 4-8 socket installations, so your 8 threads will

[gmx-users] What's the point of adding ions to neutralize the system?

Since the ion added is usually very far away from the protein (or molecule of interest), I don't see how it can affect the results of the molecular dynamics simulation. So why is it so important to add ions to neutralize the net-charge of the system?

Re: [gmx-users] AIX XLC Gromacs-5.1-rc1. Undefined reference. Underscore issue.

Hello Mark! Thank you for your advice! I'm now using Gromacs-5.1. I've added -DGMX_BUILD_MDRUN_ONLY=ON on the previous cmake configuration. Here's my cmake and error log now: export TPREFIX=/home/ibm/softwares/gromacs/xlc/vsx/omp1/flagO0/ export flags1=-qnoinline -O0 -qsmp=omp export

Re: [gmx-users] AIX XLC Gromacs-5.1-rc1. Undefined reference. Underscore issue.

Hi, Using -DGMX_FFT_LIBRARY=essl is not meaningful (per install guide), and frankly it's a build-system bug if it doesn't give a fatal error :-) That's likely the reason for the undefined symbols for the GROMACS wrapper functions that call the underlying FFT library (and that the conditional

Re: [gmx-users] What's the point of adding ions to neutralize the system?

You said it yourself: to neutralize the net charge of the system. Victor 2015-08-20 14:58 GMT-05:00 Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu : Since the ion added is usually very far away from the protein (or molecule of interest), I don't see how it can affect the results of the

Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...

On 8/20/15 4:29 PM, Jorge Fernandez de Cossio Diaz wrote: Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy

Re: [gmx-users] simulations of ice beginning to spin

Hello, I'm sorry to submit a query twice, but I have not received a reply since last week. The original message is below. As the subject line states, my simulations are developing a rotation that I cannot explain. I was wondering if the box size could be an issue, so I redid both simulations

Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded

On 8/20/15 5:21 PM, Jorge Fernandez de Cossio Diaz wrote: Note that I am adding position restrains to fix all the termini of the incomplete fragments. Shouldn't that take care of the missing residues? If there's a bond between residues that are separated by a large gap, the magnitude of

Re: [gmx-users] Non Periodic Coordinate File

On 8/20/15 5:59 PM, ANAND AMITKUMAR Dharia wrote: Hello, I was wondering if it was possible to create a non-periodic coordinate file using trjconv or some other gromacs program on a trajectory file. I would like to use coordinate data to calculate displacement in order to compute a

Re: [gmx-users] simulations of ice beginning to spin

Hello Nathan, Did you set comm-mode and nstcomm http://manual.gromacs.org/online/mdp_opt.html#run in your mdp file? Best, Eric On Thu, Aug 20, 2015 at 3:37 PM, Nathan K Houtz nho...@purdue.edu wrote: Hello, I'm sorry to submit a query twice, but I have not received a reply since last week.

[gmx-users] Non Periodic Coordinate File

Hello, I was wondering if it was possible to create a non-periodic coordinate file using trjconv or some other gromacs program on a trajectory file. I would like to use coordinate data to calculate displacement in order to compute a crosscorrelation between molecules, however, with the jumps in

Re: [gmx-users] Non Periodic Coordinate File

Wow, thank you so much, don't know how I didn't realize this. On Thu, Aug 20, 2015 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/20/15 5:59 PM, ANAND AMITKUMAR Dharia wrote: Hello, I was wondering if it was possible to create a non-periodic coordinate file using trjconv or some

Re: [gmx-users] Incorrect number of parameters - found 3, expected 1 or 1 for Polarization.

Thank you professor Justin! I solved this error which comes from the decimals of the box dimensions. Initially, my box dimensions are 4.5*4.5*16 nm3 and the local pressure calculation does not work, but after I change them to be integers 4*4*16 nm3 in the gro file, the simulation works. It is

Re: [gmx-users] Problem compiling Gromacs 5.1

Just use your favourite text editor. Peter On Thu, Aug 20, 2015 at 3:10 AM, atsutoshi0...@gmail.com wrote: Line 52 of cmake/FindSphinx.cmake file is written below. string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1 SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE}) Can you tell

[gmx-users] Adding HSD residue to AMBER ff99SB-ILDN

Hi everyone, I have a .pdb file of the WW domain of human FIP35 protein extracted from an MD calculation obtained with AMBER ff99SB-ILDN and solvent type tip3. Now I need to obtain the topology out of it, but the .pdb contains a residue, namely HSD, which is not present in the Amber residue

Re: [gmx-users] High load imbalance: 31.8%

On Thu, Aug 20, 2015 at 5:52 PM, Szilárd Páll pall.szil...@gmail.com wrote: Hi, You're not pinning threads and it seems that you're running on a large SMP machine! Assuming that the 512 threads reported (line 91) is correct that's a 32 socket SMP machine, perhaps an SGI UV? In any case Xeon

[gmx-users] Fatal error: Index contains atom numbers larger than the topology

Hi! I am running a DoS calculation using g_dos on 5.0.6 version, using the .tpr used to generate a .trr trajectory. Hence, the topology and index should contain the same number of atoms and I confirmed this by looking the number of atoms on the generated .gro. Still, I got the error: Command =

Re: [gmx-users] High load imbalance: 31.8%

Hi Szilárd Thanks for all of that advice. I’m going to have to take a lot of this up with the Cluster Service Staff. This is a new cluster service I won a grant for, thus not my usual platform which would typically yield an imbalance of somewhere around 0.8% to 2%. Thanks again Anthony On

Re: [gmx-users] Fatal error: Index contains atom numbers larger than the topology

On 8/20/15 12:12 PM, Marcelo Depólo wrote: Hi! I am running a DoS calculation using g_dos on 5.0.6 version, using the .tpr used to generate a .trr trajectory. Hence, the topology and index should contain the same number of atoms and I confirmed this by looking the number of atoms on the