[gmx-users] PRODRG -cgnr

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 will use my first way mentioned in my previous

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

I plan to put some more of this kind of documentation in the upcoming User Guide, but it isn't done yet. Number of times that section was entered, the total wall time spent in that section, and the total number of processor gigacycles spent in that section, and percentage of same. Some columns

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

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 sjyz...@gmail.com wrote: Core t (s) Wall t (s)(%) Time: 2345.800 49.744 4715.7

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:

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

[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 gromacs bin

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

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

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] 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,

[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

[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

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

[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

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

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 atila.petros...@gmail.com wrote: Dear Justin Thanks for your answer.

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 recently

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

[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

[gmx-users] subscription request

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

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

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

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

[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

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

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 md...@wesleyan.edu wrote: Hi there, I am having problems with extending my simulation after changing the .mdp file options in GROMACS 4.6. As per the

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# sukriti...@e.ntu.edu.sg wrote: Dear Gromacs users, I wanted to simulate metal ions in gromacs. For Fe+2, I

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 ac...@energiaq.com wrote: Dear gromacs users: is there any gromacs command that can allow us to compute the

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 qia...@gmail.com 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

[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] 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

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 mark.j.abra...@gmail.com wrote: On Sat, Jul 26, 2014 at 7:35 PM, Seyyed Mohtadin Hashemi haa...@gmail.com wrote: On Jul 26, 2014 4:52 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, That is indeed very weird - particularly if

[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 =

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 jalem...@vt.edu 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

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 mark.j.abra...@gmail.com wrote: On Mon, Jul 28, 2014 at 6:05 PM, qiaobf qia...@gmail.com 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

Re: [gmx-users] neighbor list

On Mon, Jul 28, 2014 at 8:27 PM, Sikandar Mashayak symasha...@gmail.com 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

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

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

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

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

On Mon, Jul 28, 2014 at 6:48 AM, Theodore Si sjyz...@gmail.com 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

Re: [gmx-users] neighbor list

Thanks Mark. That helps. -- Sikandar On Mon, Jul 28, 2014 at 1:58 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Jul 28, 2014 at 8:27 PM, Sikandar Mashayak symasha...@gmail.com wrote: Hi, I need to set up a simulation of LJ system, such that neighbor list is built using

[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