[gmx-users] TIP5P and cg minimization

[rob yang]

Thanks Mark for the pointer. 

The TIP5P.itp has [settles] only, whereas TIP4P.itp (as well as spc.itp, and TIP3P) has parameters for flexible water [FLEXIBLE] as well as rigid [settles]. This, by definition would restrict any systems using TIP5P to the SHAKE algorithm. I am wondering:
1) are there other TIP5P.itp files that possibly include the FLEXIBLE parameters (force constants for bonds and angles)?
2) for my present TIP5P.itp, is this going to impact the MD run?

I've copied and pasted my TIP5P.itp and TIP4P.itp files that I have below. Thank you very much. 

TIP5P.itp:
----------------------------
[ moleculetype ]
; molname       nrexcl
SOL             2

[ atoms ]
; id    at type res nr  residu name     at name         cg nr   charge
1       opls_118     1       SOL              OW             1       0
2       opls_119     1       SOL             HW1             1       0.241
3       opls_119     1       SOL             HW2             1       0.241
4       opls_120     1       SOL             LP1             1      -0.241
5       opls_120     1       SOL             LP2             1      -0.241

[ settles ]
; i     funct   doh     dhh
1       1       0.09572 0.15139

[ dummies3 ]

; Dummy from                    funct   a       b               c
4       1       2       3       4       -0.344908  -0.344908  -6.4437903493
5       1       2       3       4       -0.344908  -0.344908   6.4437903493

[ exclusions ]
1       2       3       4       5
2       1       3       4       5
3       1       2       4       5
4       1       2       3       5
5       1       2       3       4
---------------------------------
TIP4P.itp
---------------------------------
[ moleculetype ]
; molname	nrexcl
SOL		2

[ atoms ]
; id	at type	res nr 	residu name	at name	cg nr	charge
1	opls_113	1	SOL	 OW	1       0.0
2	opls_114	1	SOL	HW1	1	0.52
3	opls_114	1	SOL	HW2	1	0.52
4	opls_115	1	SOL	 MW	1      -1.04

#ifdef FLEXIBLE
[ bonds ]
; i	j	funct	length	force.c.
1	2	1	0.09572	502416.0 0.09572	502416.0 
1	3	1	0.09572	502416.0 0.09572	502416.0 
	
[ angles ]
; i	j	k	funct	angle	force.c.
2	1	3	1	104.52	628.02	104.52	628.02	

#else
[ settles ]
; OW    funct   doh        dhh
1       1       0.09572    0.15139
#endif

[ exclusions ]
1	2	3	4
2	1	3	4
3	1	2	4
4	1	2	3

[ dummies3 ]
; Dummy from			funct	a		b
4	1	2	3	1	0.128012065	0.128012065





----------------------------------------
> Date: Thu, 6 Mar 2008 17:15:36 +1100
> Subject: Re: [gmx-users] TIP5P and cg minimization
> From: mark.abraham at anu.edu.au
> To: gmx-users at gromacs.org
> 
>>
>> Hi list,
>> I have solvated my protein in TIP5P box that's provided by 3.3.3. However,
>> when I try to run an energy minimization using cg (at the grompp stage), I
>> get:
>> ERROR: can not do Conjugate Gradients with constraints (218328)
>>
>> I don't have any problem using the same em.mdp file on TIP4P, so I figured
>> it has something to do with TIP5P. Steep descent works, but it bugs me
>> that cg wouldn't work. As far as I can tell, there's no constraints in my
>> em.mdp file and my *.top (*.itp files too). Has anybody else encounter the
>> same problem? Thank you in advance.
> 
> [ settles ] are constraints. Check for them.
> 
> Mark
> 
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