[gmx-users] measuring surface tension

Dear gmx users, Is it possible to measure surface tension with time in a protein adsorption process at oil-water interface in Gromacs? if yes how, any help is highly appreciated. Cheers David -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Li

[gmx-users] g_select position variables

Hi everyone, Is it possible to use a position variable in conjunction with x,y,z keywords in g_select? I'm trying to select all molecules within a channel embedded in a membrane. In case the protein and/or membrane moves around I want to use position variables instead of numerical values to de

Re: [gmx-users] neighbor list

Thanks Mark. That helps. -- Sikandar On Mon, Jul 28, 2014 at 1:58 PM, Mark Abraham wrote: > On Mon, Jul 28, 2014 at 8:27 PM, Sikandar Mashayak > wrote: > > > Hi, > > > > I need to set up a simulation of LJ system, such that neighbor list is > > built using grid algorithm with a cut-off of lj_

[gmx-users] g_tcaf

Dear GROMACS Users: I would like to use the g_tcaf command to compute the viscosity of ionic liquid. I found out (searched online) that the g_tcaf command has some problems. I used the following command g_tcaf -f traj.trr -s NPT.tpr -n index.ndx -oa tcaf.xvg But got error messages. Does anybod

Re: [gmx-users] Some columns in log file.

For example, a form that explains the meanings of the all items in the log file. I found this page (http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/Topology_preparation,_%22What's_in_a_log_file%22,_basic_performance_improvements%3A_Mark_Abraham,_Session_1A)

Re: [gmx-users] Some columns in log file.

On Mon, Jul 28, 2014 at 6:48 AM, Theodore Si wrote: > Hi all, > > In the log file, what do count, wall t(s) G-Cycles mean? It seems that > the last column is the percentage of G-Cycles. "Wall t (s)" = wall-clock time spent in the respective part of code "G-cycles" = total giga- CPU cycles across

[gmx-users] Details about using g_wham

Dear GMX-Users, I’m trying to obtain free energy profile of small molecule penetration through POPC membrane. To do that, many researchers simulate using Umbrella Sampling with G_Wham analysis. (Reference : 'convergence of free energy profile of coumarin in lipid bilayer’, Michal Otypeka) Most

Re: [gmx-users] Pull code with dummy atom as reference - not working

On 7/28/14, 7:18 PM, Stella Nickerson wrote: Thanks, using direction geometry worked well. Since you seem to be very knowledgeable about this particular area, would you mind another question--When my particle passes through the less viscous to the more viscous liquid, it hovers at the interfac

Re: [gmx-users] Pull code with dummy atom as reference - not working

Thanks, using direction geometry worked well. Since you seem to be very knowledgeable about this particular area, would you mind another question--When my particle passes through the less viscous to the more viscous liquid, it hovers at the interface for several picoseconds before bursting forward

Re: [gmx-users] how to compile and make a C analyzing code under GROMACS 5.0

Hi All, One update: The first problem regarding the math library has been solved by changed: target_link_libraries(g_density2 ${GROMACS_LIBRARIES}) to target_link_libraries(g_density2 ${GROMACS_LIBRARIES}*m*) However, the 2nd problem regarding displaying the INSTRUCTION text has not solved

Re: [gmx-users] neighbor list

On Mon, Jul 28, 2014 at 8:27 PM, Sikandar Mashayak wrote: > Hi, > > I need to set up a simulation of LJ system, such that neighbor list is > built using grid algorithm with a cut-off of lj_cut_off + 0.1 every 20 > timesteps. > So, you want a single-range scheme with an explicit buffer. This will

Re: [gmx-users] how to compile and make a C analyzing code under GROMACS 5.0

Hi, On Mon, Jul 28, 2014 at 7:45 PM, Mark Abraham wrote: > On Mon, Jul 28, 2014 at 6:05 PM, qiaobf wrote: > > 2) If the line with "sqrt" function is commented out, the g_density2 can > > be successfully generated. however, the "./g_density2 -h" is not working > to > > display the help contents

Re: [gmx-users] Changing .mdp options in continuation run problems

I adjusted it and it worked! Thank you so much. On Mon, Jul 28, 2014 at 1:23 PM, Justin Lemkul wrote: > > > On 7/28/14, 1:21 PM, Matthew D Kim wrote: > >> Hi there, >> >> I am having problems with extending my simulation after changing the .mdp >> file options in GROMACS 4.6. >> As per the inst

[gmx-users] neighbor list

Hi, I need to set up a simulation of LJ system, such that neighbor list is built using grid algorithm with a cut-off of lj_cut_off + 0.1 every 20 timesteps. So I am wondering what should be the accurate settings in the grompp.mdp file. After reading the manual, I understand rvdw must be >= rlist

Re: [gmx-users] Can't run v. 4.6.6 on worker nodes if they are compiled with SIMD

On Sat, Jul 26, 2014 at 1:53 PM, Mark Abraham wrote: > On Sat, Jul 26, 2014 at 7:35 PM, Seyyed Mohtadin Hashemi > > wrote: > > > On Jul 26, 2014 4:52 AM, "Mark Abraham" > wrote: > > > > > > Hi, > > > > > > That is indeed very weird - particularly if compiling on the compute > > nodes > > > with

Re: [gmx-users] Changing .mdp options in continuation run problems

On 7/28/14, 1:21 PM, Matthew D Kim wrote: Hi there, I am having problems with extending my simulation after changing the .mdp file options in GROMACS 4.6. As per the instructions in the online Manual, I did *grompp -p system.top -f md.npt-gpu-mod.mdp -c 300monolayer.tpr -o x340monolayer.tpr -

[gmx-users] Changing .mdp options in continuation run problems

Hi there, I am having problems with extending my simulation after changing the .mdp file options in GROMACS 4.6. As per the instructions in the online Manual, I did *grompp -p system.top -f md.npt-gpu-mod.mdp -c 300monolayer.tpr -o x340monolayer.tpr -t 300monolayer.cpt* [*note: I had to specify

Re: [gmx-users] how to compile and make a C analyzing code under GROMACS 5.0

On Mon, Jul 28, 2014 at 6:05 PM, qiaobf wrote: > Dear Mark, > > Thanks a lot for your kind help. I have corrected the linkages to the > heading files. However, I got a few more problems: > 1) The math library is not recognized when compiling. See below for the > error message. Is there a way to

Re: [gmx-users] maximum energy in ipnic liquid

There is no "command", but your can obviously compute formation energy of your structure. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Mon, Jul 28, 2014 at 6:05 PM, Andy Chao wrote: > Dear gromacs users: > > is there any gromacs command that can allow us to compute the maximum > allowable

Re: [gmx-users] Lennard jones parameters for ions

Ionic and atomic radii are the same..? Wow! You should reparametrize Fe(+++) obviously. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Fri, Jul 25, 2014 at 1:39 PM, #SUKRITI GUPTA# wrote: > Dear Gromacs users, > > > I wanted to simulate metal ions in gromacs. For Fe+2, I have lj potential >

Re: [gmx-users] PRODRG -cgnr

Oh gosh sorry, I accidentally replied to someone's post rather than starting a new thread. On Mon, Jul 28, 2014 at 12:16 PM, Matthew D Kim wrote: > Hi there, > > I am having problems with extending my simulation after changing the .mdp > file options in GROMACS 4.6. > As per the instructions in

Re: [gmx-users] PRODRG -cgnr

Hi there, I am having problems with extending my simulation after changing the .mdp file options in GROMACS 4.6. As per the instructions in the online Manual, I did *grompp -p system.top -f md.npt-gpu-mod.mdp -c 300monolayer.tpr -o x340monolayer.tpr -t 300monolayer.cpt* [*note: I had to specify

[gmx-users] maximum energy in ipnic liquid

Dear gromacs users: is there any gromacs command that can allow us to compute the maximum allowable energy that can be sustained on an ionic liquid structure? in other words, instead of energy minimization, we would like to compute maximum energy under stability. Thanks! Andy -- Gromacs Users

Re: [gmx-users] how to compile and make a C analyzing code under GROMACS 5.0

Dear Mark, Thanks a lot for your kind help. I have corrected the linkages to the heading files. However, I got a few more problems: 1) The math library is not recognized when compiling. See below for the error message. Is there a way to add the flag of "-lm" under cmake? For instance, "gcc te

Re: [gmx-users] PRODRG -cgnr

On 7/28/14, 10:06 AM, Atila Petrosian wrote: Dear Justin Thanks for your quick answers. Based on your answers, what should Ido? You have more experience than me in these regards. What is your suggestion about my ligand molecule? Gromos96 parametrization is predicated upon transferring pie

Re: [gmx-users] subscription request

On 7/28/14, 11:37 AM, nicola staffolani wrote: Hi, I would like to be subscribed to this email list. If you can post, then you're subscribed. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of

[gmx-users] subscription request

Hi, I would like to be subscribed to this email list. Regards, ​Nicola​ -- Nicola Staffolani PhD Biophysics & Nanoscience Centre CNISM Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27;

[gmx-users] PRODRG -cgnr

Dear Justin Thanks for your quick answers. Based on your answers, what should Ido? You have more experience than me in these regards. What is your suggestion about my ligand molecule? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

Re: [gmx-users] PRODRG -cgnr

On 7/28/14, 8:41 AM, Atila Petrosian wrote: Dear Justin Unfortunately, now I don't access the file-sharing system. My ligand molecule is in the below link: http://en.wikipedia.org/wiki/Isoniazid Please check it. The hydrazide moiety will be your biggest challenge. While you can piece th

Re: [gmx-users] tpbconv tool change - gromacs 5.0

Dear Justin, thank you very much for your help! Have a good day, Mattia > Date: Mon, 28 Jul 2014 07:52:15 -0400 > From: jalem...@vt.edu > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] tpbconv tool change - gromacs 5.0 > > > > On 7/28/14, 4:45 AM, mattia B. wrote: > > Dear all, > > I

Re: [gmx-users] PRODRG -cgnr

Dear Justin Unfortunately, now I don't access the file-sharing system. My ligand molecule is in the below link: http://en.wikipedia.org/wiki/Isoniazid Please check it. On Mon, Jul 28, 2014 at 4:53 PM, Atila Petrosian wrote: > Dear Justin > > Thanks for your answer. > > I'm beginner in this

Re: [gmx-users] PRODRG -cgnr

On 7/28/14, 8:23 AM, Atila Petrosian wrote: Dear Justin Thanks for your answer. I'm beginner in this regard. I'm not sure . I think that my molecule is comprised almost of existing functional groups. I attached picture of my molecule to this email. please check it. The list does not accep

[gmx-users] PRODRG -cgnr

Dear Justin Thanks for your answer. I'm beginner in this regard. I'm not sure . I think that my molecule is comprised almost of existing functional groups. I attached picture of my molecule to this email. please check it. Please help me to do this issue correctly. Thanks for your time and cons

Re: [gmx-users] Error in system_inflate.gro coordinates does not match

On 7/28/14, 1:42 AM, RINU KHATTRI wrote: hello everyone i used editconf editconf -f protein.gro -o protein_newbox.gro -box (membrane box vectors) -center *x y z* but in z axis i have been increased box size 10. (previously it is 6.23910 6.17970 6.91950 http://s48.photobucket.com/user/

[gmx-users] IR spectra, X-ray diffraction

Hi guys. Do you know of any way to simulate IR- & X-ray spectra with GROMACS? -- 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)subsc

[gmx-users] FEP and equilibration problems

Hi, I'm having problems with running a FEP decoupling procedure for my POPE, protein and ligand system. I'm following the Alchemistry.org Gromacs 4.6 tutorial ( http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme) while changing the necessary paramete

Re: [gmx-users] PRODRG -cgnr

On 7/28/14, 2:05 AM, Atila Petrosian wrote: Dear Justin Thanks for your answer. I want to use GROMOS96 43a1 force field for my protein and PRODRG parameters for my ligand. I want to use leap-frog algorithm for integrator. Based on your opinion, I don't use QM charges. In these conditions, I

Re: [gmx-users] tpbconv tool change - gromacs 5.0

On 7/28/14, 4:45 AM, mattia B. wrote: Dear all, I recently moved from gromacs 4.6 to version 5.0. When I run the command tpbconv, I get the message "This tool has been removed from Gromacs 5.0". The "tool changes for 5.0" page says the command has been renamed in "gmx convert-tpr". However, I

Re: [gmx-users] g_cluster analysis for structure refirement

Thanks! That was very usefull. BTW have someone tried some software for visualization of such clusters and compution of the percents of the SS elements in each cluster (for instance by comparison of the most representative structures from each cluster etc). Might this VMD plugin http://physiology

Re: [gmx-users] How do I get to know the meaning of the first column in log file?

Hi all, Could anyone explain all the meanings of these columns in log? I'd appreciate your help. Domain decomp. DD comm. load DD comm. bounds Send X to PME Neighbor search Comm. coord. Force Wait + Comm. F PME mesh PME wait for PP Wait + Recv. PME F NB X/F buffer ops. Write traj. Update Constrai

[gmx-users] tpbconv tool change - gromacs 5.0

Dear all, I recently moved from gromacs 4.6 to version 5.0. When I run the command tpbconv, I get the message "This tool has been removed from Gromacs 5.0". The "tool changes for 5.0" page says the command has been renamed in "gmx convert-tpr". However, I cannot find this executable in my gromac

Re: [gmx-users] How do I get to know the meaning of the first column in log file?

Hi, if you need 0.345 hour to get 1 ns, that means that you can simulate 1/0.345~2.9ns/hour, then in one day you will simulate 1/0.345*24~69.5 ns Guillaume On 07/28/2014 09:39 AM, Theodore Si wrote: I thought that 69.479 ns/day means I can simulate 69.479 ns per day. But if as you said, I ne

Re: [gmx-users] How do I get to know the meaning of the first column in log file?

I thought that 69.479 ns/day means I can simulate 69.479 ns per day. But if as you said, I need 0.345 hour to get a simulated nanosecond, then I can only get 0.345 * 24 = 8.28 simulated nanosecond per day? Then what does 69.479 mean? And the Core t(s)? 于 2014/7/28 15:29, Mark Abraham 写道: You

Re: [gmx-users] How do I get to know the meaning of the first column in log file?

Your run took nearly a minute, and did so at a rate that would take 0.345 hours to do a simulated nanosecond Mark On Mon, Jul 28, 2014 at 9:05 AM, Theodore Si wrote: >Core t (s) Wall t (s)(%) >Time: 2345.800 49.744 4715.7 > (ns/d

Re: [gmx-users] How do I get to know the meaning of the first column in log file?

Core t (s) Wall t (s)(%) Time: 2345.800 49.744 4715.7 (ns/day)(hour/ns) Performance: 69.4790.345 What does 0.345 hour/ns stand for? and the Wall time 49.77s? 于 2014/7/28 14:53, Mark Abraham 写道: I plan to put some