Re: [gmx-users] Re: The molecule size (jiqing)
》Has this force field been demonstrated to be effective for this sort ofsimulation? If not, maybe you've begun to demonstrate that it isn't?Mark Yes , you are quite right. In GMX manual 3.2, at the end of chapter 4, it was said thatgromos96 is not, however, recommended for use with long alkanes and lipids. So user has to validate force parameters. Now the problem is for a periodic boundary system, the density is ok but the Rg is too small. I feel the parameters for proper dihedrals need to be improved. Is it right? *Ji QingInstitute of Chemistry, Chinese Academy of SciencesTel: 0086-10-62562894 ，82618423* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The molecule size
Hi: Two melt models were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition . The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept as follows. The Rg for PE (C1000) is just 28 angstrom. It means the infinite charaterastic ratio (Cinf) for the polymer is just about 2 which is much smaller than scatter experimental value about 7. The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for the polymer is just 2.5 which is much smaller than scatter experimental value 8-10. Can these results be accepted? Is there any fault in force field? gromos96aUsually a garbage result as output means that you had either garbage asinput, or garbage for the algorithm. Find a published article thatdescribes a similar simulation and adapt their method suitably.Otherwise describe your method more thoroughly (e.g. how large was thebox, what ensemble did you use, equilibration regime, etc.) and maybesomeone has some judgement they can share with you.Mark Hi Mark: Thanks for your advise. Because the PE model is built by one of my officemate, i did not konw its details. The cell length about my PVME model is 4.5 nm which is big enough for a PVME chain possesses all trans conformation. The ensemble is NVT with the control file Pcoupl= no after 10ns NPT simulation to reach the experimental density. The runtime for NVT is 5ns from which the relax time for end to end vector is anaylzed. The relax time is about 1ns. So i think the system has been relaxed enough. Is there any error in my process? Maybe the residue parameter for PVME is also needed for discuss. They are: [ VME ] [ atoms ] ; atom type charge cgnr CN Gasteiger CAB CH1 0.142 1 ; CN CAA CH2 0.035 1 ; CN OAD OE -0.352 1 ; CN CAC CH3 0.174 1 ; CN [ bonds ] ; ai aj fu CAA CAB gb_27 CAB OAD gb_53 CAC OAD gb_53 CAB +CAA gb_27 [ angles ] ; ai aj ak fu c0, c1, ... CAA CAB OAD ga_30 CAB OAD CAC ga_10 OAD CAB +CAA ga_30 CAA CAB +CAA ga_15 CAB +CAA +CAB ga_15 [ dihedrals ]; ai aj ak al fu c0, c1, m, ... CAA CAB OAD CAC gd_13 CAA CAB +CAA +CAB gd_34+CAA CAB OAD CAC gd_13CAB +CAA +CAB +OAD gd_1 *Ji QingInstitute of Chemistry, Chinese Academy of SciencesTel: 0086-10-62562894 ，82618423* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: The molecule size (jiqing)
Hi:Two melt models were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition .The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept as follows.The Rg for PE (C1000) is just 28 angstrom. It means the infinite charaterastic ratio (Cinf) for the polymer is just about 2 which is much smaller than scatter experimental value about 7.The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for the polymer is just 2.5 which is much smaller than scatter experimental value 8-10.Can these results be accepted?Is there any fault in force field? gromos96aTwo things,- maybe you need a larger systems- maybe g_gyrate does not take periodicity into account correctly. extract some single molecules and look at them in a viewer, or write your own script to compute Rg.- have you used pbc = full for the simulations? 1.The cell length about my PVME model is 4.5 nm which is big enough for a PVME chain possesses all trans conformation. 2. The Rg is anaylzed by my own program, which has been validated. 3.PBC=XYZ Usually a garbage result as output means that you had either garbage as input, or garbage for the algorithm. Find a published article that describes a similar simulation and adapt their method suitably. Otherwise describe your method more thoroughly (e.g. how large was the box, what ensemble did you use, equilibration regime, etc.) and maybe someone has some judgement they can share with you. Mark *Hi Mark:* *Thanks for your advise. Because the PE model is built by one of my officemate, i did not konw its details.* ** *The cell length about my PVME model is 4.5 nm which is big enough for a PVME chain possesses all trans conformation. The ensemble is NVT with the control file Pcoupl = no after 10ns NPT simulation to reach the experimental density. The runtime for NVT is 5ns from which the relax time for end to end vector is anaylzed. The relax time is about 1ns. So i think the system has been relaxed enough.* ** *Is there any error in my process?* ** *Maybe the residue parameter for PVME is also needed for discuss. They are:* [ VME ] [ atoms ] ; atom type charge cgnr CN Gasteiger CAB CH1 0.142 1 ; CN CAA CH2 0.035 1 ; CN OAD OE -0.352 1 ; CN CAC CH3 0.174 1 ; CN [ bonds ] ; ai aj fu CAA CAB gb_27 CAB OAD gb_53 CAC OAD gb_53 CAB +CAA gb_27 [ angles ] ; ai aj ak fu c0, c1, ... CAA CAB OAD ga_30 CAB OAD CAC ga_10 OAD CAB +CAA ga_30 CAA CAB +CAA ga_15 CAB +CAA +CAB ga_15 [ dihedrals ]; ai aj ak al fu c0, c1, m, ... CAA CAB OAD CAC gd_13 CAA CAB +CAA +CAB gd_34+CAA CAB OAD CAC gd_13CAB +CAA +CAB +OAD gd_1 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] The molecule size
Hi: Two meltmodels were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition. The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept as follows. The Rg for PE (C1000) is just 28 angstrom. It means the infinite charaterastic ratio (Cinf) for the polymer is just about 2 which is much smaller than scatter experimental value about 7. The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for the polymer is just 2.5 which is much smaller than scatter experimental value 8-10. Can these results be accepted? Is there any fault in force field? gromos96a Thanks in advance. *Ji QingInstitute of Chemistry, Chinese Academy of SciencesTel: 0086-10-62562894 ，82618423* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Tip5p with gromos 96, error atom has mass 0
Hi all: I built a topol file for tip5p water accordint to tip5p.itp which is designed for OPLS.But when i used grompp to built a tpr file,three errors came even the system just have one tip5p water. The error is : ERROR 1 [file "topol.top", line 10]: atom OW Res SOL-1 has mass 0 ERROR2 [file "topol.top", line 10]: atomHW1 Res SOL-1 has mass 0 ERROR3 [file "topol.top", line 10]: atomHW2 Res SOL-1 has mass 0 In fact, the mass for all above atoms were all defined in atp file. How can i fix it? Thanks a lot. The build steps are follows: 1.Named the atom type in new tip5p.itp. Add them to ffG53a6.atp and ffG53a6nb.itp. In tip5p.itp: [ atoms ]; id at type res nr residu name at name cg nr charge1 5p_O 1 SOL OW 1 02 5p_H 1 SOL HW1 1 0.2413 5p_H 1 SOL HW2 1 0.2414 5p_L 1 SOL OL1 1 -0.2415 5p_L 1 SOL OL2 1 -0.241 In ffG53a6.atp 5p_O 15.99940 ; O TIP5P Water5p_H 1.00800 ; H TIP5P Water5p_L 0.0 ; L TIP5P Water In ffG53a6nb.itp 5p_O 80.000 0.000 A 2.470013e-03 2.278383e-065p_H 10.000 0.000 A 0 05p_L 00.000 0.000 D 0 0 2. Write top file. #include "ffG53a6.itp"#include "tip5p_.itp" [ system ]; NameProtein [ molecules ]; Compound #molsSOL 1 3. Built gro 5 1SOL OW 1 0.321 1.614 0.603 1SOL HW1 2 0.377 1.643 0.675 1SOL HW2 3 0.258 1.555 0.645 1SOL OL1 4 0.358 1.581 0.554 1SOL OL2 5 0.288 1.669 0.574 0.5 0.5 0.54. grompp -f em.mdp Then the errors came. *Ji QingInstitute of Chemistry, Chinese Academy of SciencesTel: 0086-10-62562894 ，82618423* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] tip4p or 5p
I want to build a water cell with 4p or 5p.How can i realized it? May be after include *.itp in current top, something need to be modified? It was said that 4p or 5p need OPLS together. How can i used it in GROMOS 96 *Ji QingInstitute of Chemistry, Chinese Academy of SciencesTel: 0086-10-62562894 ，82618423* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] The water model with tip5p in gromos96
Hi everyone: I found that in tip5p.itp, there is a note tell user to use tip5p model with opls force field. Butwhat i really want to use is the gromos96. How can i include tip5p model? Thanks a lot *Ji QingInstitute of Chemistry, Chinese Academy of SciencesTel: 0086-10-62562894 ，82618423* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: MD run end abnormally
Problem has been fixed! Just add the 'nohup' in front of 'mdrun' *Ji Qing（吉青）Institute of Chemistry, Chinese Academy of Sciences（中科院化学所）Tel: 0086-10-62562894 ，82618423* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] MD run end abnormally more detailed info
Hi : Mark, thanks for your advice. But i only use the single-processor.And the enviourment is RedHat 9.0 with gromacs 3.3.1. what is other problem of this error Date: Sun, 2 Jul 2006 15:17:53 +1000 (EST)From: "Mark Abraham" [EMAIL PROTECTED]Subject: Re: [gmx-users] MD run end abnormallyTo: "Discussion list for GROMACS users" gmx-users@gromacs.orgMessage-ID:[EMAIL PROTECTED]Content-Type: text/plain;charset=iso-8859-1 Hi: I install GMX FFTW MPI in my own folders. And then i used a begin structure which performed well at other computers to test the GMX programme. What is strange to me is that the job can run well at begginning time but after a while the CPU was not still busy, and the output file was not change. I chencked the log file. There is no reason. And i used g_energy to check the condition of MD.But the "Potential"Kinetic En." "Temperature" were all in equilibrium. Every time the error came with different step. Some time is 5 step. Some time is 2445001 . What is the error? How can i fix it.It sounds like you are using a Windows MPI environment that isn't workingproperly. Test single-processor calculations to see they work OK. If so,try to eliminate other processes running on the machines, and turn off anyauto-hibernation stuff.Mark 祝 好 *Ji Qing（吉青）Institute of Chemistry, Chinese Academy of Sciences（中科院化学所）Tel: 0086-10-62562894 ，82618423* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] MD run end abnormally
Hi: I install GMX FFTW MPIin my own folders. And then i used a begin structure which performedwell at other computers to test the GMX programme. What is strange to me is that the job can run well atbegginning time but after a while theCPU was not still busy, and the output filewas not change.I chencked thelog file.There is no reason. And i usedg_energy to check the condition of MD.But the "Potential"Kinetic En." "Temperature" were all in equilibrium. Every time the error came with different step. Sometime is 5 step. Some time is 2445001 . What is the error? How can i fix it. Thanks in advance. 祝 好 *Ji Qing（吉青）Institute of Chemistry, Chinese Academy of Sciences（中科院化学所）Tel: 0086-10-62562894 ，82618423* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] compile GMX source code by VC 6.0
Hi: I tried to compile GMX source code by VC 6.0. I found the main function of MD simulation is in mdrun.c. And then i compiled it as main file. But some varier type my compiler can not find . Such as : LONG;TCHAR;BSTR; BOOL;DATE; How can i fix it ! thanks a lot ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
