Re:Re: [gmx-users] ligand-protein simulation

ot; wrote: > > >On 11/1/13 5:37 AM, xiao wrote: >> Dear all gromacs users, >> >> I have run a protein-ligand simulations. However, the position of the ligand >> is not reasonable after 10ns simulation. There is no problem with the force >> field paramers of the

Re:[gmx-users] Lysozyme in Water at different pH and Ionic strength

It is impossible. But you can add proton to the acidic amino acid. At 2013-11-01 20:36:41,Mass wrote: >Dear Gromacs users, >Just was wondering if it is possible to protein solution let say Lysozyme in >Water example of Justin tutorial at different pH and ionic strengths, if so >how? >Thanks

[gmx-users] ligand-protein simulation

Dear all gromacs users, I have run a protein-ligand simulations. However, the position of the ligand is not reasonable after 10ns simulation. There is no problem with the force field paramers of the ligand. I am trying to constrict the ligand move for 500ps simulation. But i do not know whethe

Re:Re: [gmx-users] problem with the amb2gmx.pl

Hi Alan, Thank you very much! The problem is solved. The reason is that amb2gmx cannot distinguish the proper and improper dihedrals. Best wishes Fugui At 2013-10-09 21:58:29,Alan wrote: >Hi, try ACPYPE. > >Alan > > >On 9 October 2013 14:07, xiao wrote: > >>

[gmx-users] problem with the amb2gmx.pl

Dear all, I am doing membrane protein simulation by using amber force field. The lipid force field parameters are from the lipid11.dat from Amber. Firstly, i got the xx.prmtop and xx.prmcrd files, and then i used amb2gmx.pl to convert the xx.prmtop and xx.prmcrd files into gromacs files xx.top

[gmx-users] control atom in .hdb file

Dear all, I am developing the force field paramters of an organic molecule. I have a trouble when i wrote the hydrogen atom database (.hdb) file. I do not know how to write to control atom. The manual said that: Three or four control atoms (i,j,k,l), where the first always is the atom to whic

Re:Re: [gmx-users] How to calculate the potential energy of a molecule in a fixed conformation.

Dear Justin, Thank you so much for your help! Best wishes Fugui At 2013-07-28 03:52:47,"Justin Lemkul" wrote: > > >On 7/27/13 11:48 AM, xiao wrote: >> Dear Gromacs users, >> >> I am developing the force field parameters of an organic molecule.

[gmx-users] How to calculate the potential energy of a molecule in a fixed conformation.

Dear Gromacs users, I am developing the force field parameters of an organic molecule. I need to calculate the MM energy of the molecule in a fixed conformation. For example, in order to get the force constant of a bond, i need to calculate the energy of the bond in different distance by using

Re:Re: Re: [gmx-users] Implicit solvent MD is not fast and not accurate.

Dear Justin, Thank you very much for your suggetions. BW Fugui At 2013-03-27 22:15:23,"Justin Lemkul" wrote: >On Wed, Mar 27, 2013 at 10:11 AM, xiao wrote: > >> Dear Justin, >> Thank you very much for your reply. >> I found that the speed of implict

Re:Re: [gmx-users] Implicit solvent MD is not fast and not accurate.

2013-03-27 21:45:42,"Justin Lemkul" wrote: >On Wed, Mar 27, 2013 at 9:27 AM, xiao wrote: > >> Dear Gromacs users: >> I did a protein MD using implicit solvent and Amber 99SB force filed. >> However, i found that the implicit solvent is not faster than explici

[gmx-users] Implicit solvent MD is not fast and not accurate.

Dear Gromacs users: I did a protein MD using implicit solvent and Amber 99SB force filed. However, i found that the implicit solvent is not faster than explicit solvent, and what is worse is that it is also not accurate. The system is a protein-ligand complex. Firstly, i run a minimization, and t

Re:Re: [gmx-users] problem in converting coarse grained structure to fine strcture

Dear Groetnis, Thank you very much for your nice suggestion. BW Fugui At 2013-03-26 17:34:08,"Djurre de Jong-Bruinink" wrote: >>I used the command g_fg2cg to convert a coarse grained structure into >>corresponding fine strcture, and i found that the water molecues can be >>transformed corre

[gmx-users] problem in converting coarse grained structure to fine strcture

Dear gromacs users, I used the command g_fg2cg to convert a coarse grained structure into corresponding fine strcture, and i found that the water molecues can be transformed correctly, but there is a big mess in the protien , and i could not get correct protein strcture, can anyone give me some

[gmx-users] how to convert Coarse Grained protein structure to all-atom structure

Dear gromacs users: I finished a coarse grained MD of a protein, but i cannot convert the coarse grained structure into all-atom structure, can anybody give me some advice on that? Best wishes Fugui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] helitr...@126.com

-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to g

Re: [gmx-users] the first 10 missing interactions, except for exclusions...

add dihedral parameter for you EPON molecule. Check this: http://oldwww.gromacs.org/pipermail/gmx-users/2005-May/015044.html 2010/10/24 英雄不再寂寞 > Dear gmxers, > I try to simulate a complex system using gmx-4.5.1. I have carried out > the minimization without any errors, but when it comes to

[gmx-users] Is there anyone who has tip3p.gro?

Hi there, Recently, I cannot add tip3p water in my system, because GMX cannot find tip3p.gro in GMXLIB. I am wondering is there anyone who has tip3p.gro, and could you please give me one copy. highly appreciate!! shijun -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

[gmx-users] Re: gmx-users Digest, Vol 65, Issue 122

-- > > Message: 1 > Date: Mon, 21 Sep 2009 06:24:34 + (GMT) > From: Mark Abraham > Subject: Re: [gmx-users] Re: who can help me with the force-field? > To: Discussion list for GROMACS users > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" &

[gmx-users] Re: who can help me with the force-field?

Mark wrote: > xiao shijun wrote: >> Hi everyone, >> Recently, I met a problem on the force-field. I am doing something >> on the calcium carbonate, and want to simulation it with gromacs. >> The shell model for oxygen has been emploied in my system. W

[gmx-users] who can help me with the force-field?

is no buckingham options for LJC14. I want to know if anyone of you have such the experience. Thanks!! BEST Shijun XIAO ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] What can I to do with the problem: lincs warning and water can not be settled?

hi, The simulation was OK. But when I changed the epsilon of some atoms to get rid of LJ, lincs warning emerged as: step 116 ; time 0.232 LINCS warning ralative constraint deviation after LINCS: rms 0.168368, max 4.765960 (betwe

[gmx-users] reference group in constant velocity pulling, GMX 4

any one have any idea? Thanks! -- Senbo Xiao PICB, Shanghai, 200031 CHINA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting

Re: [gmx-users] gmxtest

Hi Mark, Thanks! S. On Wed, May 27, 2009 at 12:03 PM, Mark Abraham wrote: > Mark Abraham wrote: > >> Simba Xiao wrote: >> >>> Dear all, >>> >>> Does your GMX 4 past the gmxtest package in the gmx wiki ? >>> >>> My Gromacs 4.0.4 ca

[gmx-users] gmxtest

Dear all, Does your GMX 4 past the gmxtest package in the gmx wiki ? My Gromacs 4.0.4 can not pass all the test. The test tip4p, ti4pflex and some kernel issues failed. I use standard packages and everything looks find. The simulation result are good and identical to gromacs 3.3.3. But, still

[gmx-users] g_rdf -xy

Dear Berk, I am sorry that I have a mistake in the first letter. In fact I used -bin 0.05, not 100. Yet the result is hanged. Maybe as you said, the current Gromacs can not realize what I want to do. Thanks again! H.Y. Xiao ___ gmx-users mailing

[gmx-users] g_rdf -xy

rdf -f -s -n -bin 100 -xy -o Is the runing normal? Please give me some suggestion. Thanks a lot! H.Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht

[gmx-users] prolems on viewing .trr file by vmd

very much! H.Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests t

[gmx-users] install problem

checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... configure: error: C compiler cannot create executables See `config.log' for more details. Can you help me? I hope for your answer. Thank you very much! H.Y.

[gmx-users] parallel install gromacs-4.0.4

Dear Mark, I do not understand your meaning. Can you explain it to me again? Thanks! H.Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] parallel install gromacs-4.0.4

ursive] Error 1 How to solve these problem? Hope for your help. Thank you very much! H.Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/s

[gmx-users] minimization problem

Hi, I has used the periodic boundary conditions and correct em.mdp file. However, the minimized result is water/decane/water, while I set decane/water/decane as the initial system . I cannot understand the reason. Please give me some constructive suggestion! Thanks! H. Y. Xiao

[gmx-users] minimization problem

Hi, David van der Spoel I used the periodic boundary conditions. The box is 3.006x3.002x6.000 along x,y,z direction,respectively.The following is the em.mdp file. ; ; User xiao ; 2008.9.28 10:23 ; Input file ; cpp = /usr/bin/cpp define

[gmx-users] minimization problems

water turns into two parts. I am surprised by the minimized result. Can you tell me the possible reasons? Thank you very much! H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] error range of surface tension

very much! H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list.

[gmx-users] Different potential function combination

combined? I hope for your help. Thanks a lot! H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don&#

[gmx-users] charge distribution

. what do you think so? Thanks again! H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't pos

[gmx-users] charge distribution

? I have the mulliken charge distribution and ESP charge from the quantum calculation. Should I employ them? Can you give me some advice? Thanks a lot! H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

[gmx-users] surface simulation

control the CCl4 molecule not to run to the vacuum using the gromacs? For example, using the wall, but I do not set up wall parameters well. Please give me some suggestion. Thanks again! H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] CCl4 parameters

parameters #include "ffG53a6.itp" #include "ccl4.itp" ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Pure CL4 [ molecules ] ; Compound#mols CL4169 ~ What does it lose? Please giv

[gmx-users] CCl4 parameters problem

a check the CCl4 parameters again and did not find the parameter lost. I want to know why the warning occurs? I hope for your help! Thanks! H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx

[gmx-users] surface simulation

phase. I want to know how to control CCl4 not to run to gas phase. I used the gromos96 force field. Can you help me? I expect your answer. Thanks a lot! H. Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

Re: [gmx-users] dynamics with toluene as solvent

I think you can use The Dundee PRODRG sever to generate toluene structure and topology for gromacs, but use it with care. On 9/21/07, Eva Santos <[EMAIL PROTECTED]> wrote: > > > Hello everyone, > > I need to do some molecular dynamics, using gromos96 force field, with > toluene as solvent. > I ha